1
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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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2
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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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3
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Xiao Z, Zha J, Yang X, Huang T, Huang S, Liu Q, Wang X, Zhong J, Zheng J, Liang R, Deng Z, Zhang J, Lin S, Dai S. A three-level regulatory mechanism of the aldo-keto reductase subfamily AKR12D. Nat Commun 2024; 15:2128. [PMID: 38459030 PMCID: PMC10923870 DOI: 10.1038/s41467-024-46363-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: 08/11/2023] [Accepted: 02/23/2024] [Indexed: 03/10/2024] Open
Abstract
Modulation of protein function through allosteric regulation is central in biology, but biomacromolecular systems involving multiple subunits and ligands may exhibit complex regulatory mechanisms at different levels, which remain poorly understood. Here, we discover an aldo-keto reductase termed AKRtyl and present its three-level regulatory mechanism. Specifically, by combining steady-state and transient kinetics, X-ray crystallography and molecular dynamics simulation, we demonstrate that AKRtyl exhibits a positive synergy mediated by an unusual Monod-Wyman-Changeux (MWC) paradigm of allosteric regulation at low concentrations of the cofactor NADPH, but an inhibitory effect at high concentrations is observed. While the substrate tylosin binds at a remote allosteric site with positive cooperativity. We further reveal that these regulatory mechanisms are conserved in AKR12D subfamily, and that substrate cooperativity is common in AKRs across three kingdoms of life. This work provides an intriguing example for understanding complex allosteric regulatory networks.
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Affiliation(s)
- Zhihong Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Jinyin Zha
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xu Yang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Tingting Huang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Shuxin Huang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Qi Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Xiaozheng Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Jie Zhong
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jianting Zheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Rubing Liang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Jian Zhang
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
- Haihe Laboratory of Synthetic Biology, Tianjin, 300308, China.
- Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Shaobo Dai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
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4
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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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5
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Bányai A, Farkas E, Jankovics H, Székács I, Tóth EL, Vonderviszt F, Horváth R, Varga M, Fürjes P. Dean-Flow Affected Lateral Focusing and Separation of Particles and Cells in Periodically Inhomogeneous Microfluidic Channels. SENSORS (BASEL, SWITZERLAND) 2023; 23:800. [PMID: 36679593 PMCID: PMC9865988 DOI: 10.3390/s23020800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/29/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
The purpose of the recent work is to give a better explanation of how Dean vortices affect lateral focusing, and to understand how cell morphology can alter the focusing position compared to spherical particles. The position and extent of the focused region were investigated using polystyrene fluorescent beads with different bead diameters (Ø = 0.5, 1.1, 1.97, 2.9, 4.8, 5.4, 6.08, 10.2, 15.8, 16.5 µm) at different flow rates (0.5, 1, 2 µL/s). Size-dependent focusing generated a precise map of the equilibrium positions of the spherical beads at the end of the periodically altering channels, which gave a good benchmark for focusing multi-dimensional particles and cells. The biological samples used for experiments were rod-shaped Escherichia coli (E. coli), discoid biconcave-shaped red blood cells (RBC), round or ovoid-shaped yeast, Saccharomyces cerevisiae, and soft-irregular-shaped HeLa cancer-cell-line cells to understand how the shape of the cells affects the focusing position at the end of the channel.
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Affiliation(s)
- Anita Bányai
- Centre for Energy Research, Institute of Technical Physics and Materials Science, Eötvös Loránd Research Network, Konkoly Thege Miklós Str. 29-33, H-1121 Budapest, Hungary
- 77 Elektronika Ltd., Fehérvári Str. 98, H-1111 Budapest, Hungary
- Doctoral School on Materials Sciences and Technologies, Óbuda University, Bécsi Str. 96/B, H-1034 Budapest, Hungary
| | - Enikő Farkas
- Centre for Energy Research, Institute of Technical Physics and Materials Science, Eötvös Loránd Research Network, Konkoly Thege Miklós Str. 29-33, H-1121 Budapest, Hungary
| | - Hajnalka Jankovics
- Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, Egyetem Str. 10, H-8200 Veszprém, Hungary
| | - Inna Székács
- Centre for Energy Research, Institute of Technical Physics and Materials Science, Eötvös Loránd Research Network, Konkoly Thege Miklós Str. 29-33, H-1121 Budapest, Hungary
| | - Eszter Leelőssyné Tóth
- Centre for Energy Research, Institute of Technical Physics and Materials Science, Eötvös Loránd Research Network, Konkoly Thege Miklós Str. 29-33, H-1121 Budapest, Hungary
| | - Ferenc Vonderviszt
- Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, Egyetem Str. 10, H-8200 Veszprém, Hungary
| | - Róbert Horváth
- Centre for Energy Research, Institute of Technical Physics and Materials Science, Eötvös Loránd Research Network, Konkoly Thege Miklós Str. 29-33, H-1121 Budapest, Hungary
| | - Máté Varga
- 77 Elektronika Ltd., Fehérvári Str. 98, H-1111 Budapest, Hungary
| | - Péter Fürjes
- Centre for Energy Research, Institute of Technical Physics and Materials Science, Eötvös Loránd Research Network, Konkoly Thege Miklós Str. 29-33, H-1121 Budapest, Hungary
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6
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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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7
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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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8
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Voliotis M, Rosko J, Pilizota T, Liverpool TB. Steady-state running rate sets the speed and accuracy of accumulation of swimming bacteria. Biophys J 2022; 121:3435-3444. [PMID: 36045575 PMCID: PMC9515231 DOI: 10.1016/j.bpj.2022.08.012] [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: 01/19/2022] [Revised: 07/31/2022] [Accepted: 08/15/2022] [Indexed: 11/21/2022] Open
Abstract
We study the chemotaxis of a population of genetically identical swimming bacteria undergoing run and tumble dynamics driven by stochastic switching between clockwise and counterclockwise rotation of the flagellar rotary system, where the steady-state rate of the switching changes in different environments. Understanding chemotaxis quantitatively requires that one links the measured steady-state switching rates of the rotary system, as well as the directional changes of individual swimming bacteria in a gradient of chemoattractant/repellant, to the efficiency of a population of bacteria in moving up/down the gradient. Here we achieve this by using a probabilistic model, parametrized with our experimental data, and show that the response of a population to the gradient is complex. We find the changes to the steady-state switching rate in the absence of gradients affect the average speed of the swimming bacterial population response as well as the width of the distribution. Both must be taken into account when optimizing the overall response of the population in complex environments.
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Affiliation(s)
- Margaritis Voliotis
- College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, United Kingdom.
| | - Jerko Rosko
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Teuta Pilizota
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, United Kingdom.
| | - Tanniemola B Liverpool
- School of Mathematics, University of Bristol, Bristol, United Kingdom; BrisSynBio, Life Sciences Building, University of Bristol, Bristol, United Kingdom.
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9
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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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10
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Monteagudo-Cascales E, Santero E, Canosa I. The Regulatory Hierarchy Following Signal Integration by the CbrAB Two-Component System: Diversity of Responses and Functions. Genes (Basel) 2022; 13:genes13020375. [PMID: 35205417 PMCID: PMC8871633 DOI: 10.3390/genes13020375] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 02/04/2023] Open
Abstract
CbrAB is a two-component system, unique to bacteria of the family Pseudomonaceae, capable of integrating signals and involved in a multitude of physiological processes that allow bacterial adaptation to a wide variety of varying environmental conditions. This regulatory system provides a great metabolic versatility that results in excellent adaptability and metabolic optimization. The two-component system (TCS) CbrA-CbrB is on top of a hierarchical regulatory cascade and interacts with other regulatory systems at different levels, resulting in a robust output. Among the regulatory systems found at the same or lower levels of CbrAB are the NtrBC nitrogen availability adaptation system, the Crc/Hfq carbon catabolite repression cascade in Pseudomonas, or interactions with the GacSA TCS or alternative sigma ECF factor, such as SigX. The interplay between regulatory mechanisms controls a number of physiological processes that intervene in important aspects of bacterial adaptation and survival. These include the hierarchy in the use of carbon sources, virulence or resistance to antibiotics, stress response or definition of the bacterial lifestyle. The multiple actions of the CbrAB TCS result in an important competitive advantage.
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Affiliation(s)
| | - Eduardo Santero
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Centro Andaluz de Biología del Desarrollo, CSIC, Junta de Andalucía, 41013 Seville, Spain;
| | - Inés Canosa
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Centro Andaluz de Biología del Desarrollo, CSIC, Junta de Andalucía, 41013 Seville, Spain;
- Correspondence: ; Tel.: +34-954349052
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11
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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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12
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Skinner DJ, Dunkel J. Estimating Entropy Production from Waiting Time Distributions. PHYSICAL REVIEW LETTERS 2021; 127:198101. [PMID: 34797138 DOI: 10.1103/physrevlett.127.198101] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 08/17/2021] [Indexed: 06/13/2023]
Abstract
Living systems operate far from thermal equilibrium by converting the chemical potential of ATP into mechanical work to achieve growth, replication, or locomotion. Given time series observations of intra-, inter-, or multicellular processes, a key challenge is to detect nonequilibrium behavior and quantify the rate of free energy consumption. Obtaining reliable bounds on energy consumption and entropy production directly from experimental data remains difficult in practice, as many degrees of freedom typically are hidden to the observer, so that the accessible coarse-grained dynamics may not obviously violate detailed balance. Here, we introduce a novel method for bounding the entropy production of physical and living systems which uses only the waiting time statistics of hidden Markov processes and, hence, can be directly applied to experimental data. By determining a universal limiting curve, we infer entropy production bounds from experimental data for gene regulatory networks, mammalian behavioral dynamics, and numerous other biological processes. Further considering the asymptotic limit of increasingly precise biological timers, we estimate the necessary entropic cost of heartbeat regulation in humans, dogs, and mice.
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Affiliation(s)
- Dominic J Skinner
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA
| | - Jörn Dunkel
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA
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13
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Abstract
Living systems maintain or increase local order by working against the second law of thermodynamics. Thermodynamic consistency is restored as they consume free energy, thereby increasing the net entropy of their environment. Recently introduced estimators for the entropy production rate have provided major insights into the efficiency of important cellular processes. In experiments, however, many degrees of freedom typically remain hidden to the observer, and, in these cases, existing methods are not optimal. Here, by reformulating the problem within an optimization framework, we are able to infer improved bounds on the rate of entropy production from partial measurements of biological systems. Our approach yields provably optimal estimates given certain measurable transition statistics. In contrast to prevailing methods, the improved estimator reveals nonzero entropy production rates even when nonequilibrium processes appear time symmetric and therefore may pretend to obey detailed balance. We demonstrate the broad applicability of this framework by providing improved bounds on the energy consumption rates in a diverse range of biological systems including bacterial flagella motors, growing microtubules, and calcium oscillations within human embryonic kidney cells.
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Affiliation(s)
- Dominic J Skinner
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Jörn Dunkel
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139
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14
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Abstract
Understanding the motility behavior of bacteria in confining microenvironments, in which they search for available physical space and move in response to stimuli, is important for environmental, food industry, and biomedical applications. We studied the motility of five bacterial species with various sizes and flagellar architectures (Vibrio natriegens, Magnetococcus marinus, Pseudomonas putida, Vibrio fischeri, and Escherichia coli) in microfluidic environments presenting various levels of confinement and geometrical complexity, in the absence of external flow and concentration gradients. When the confinement is moderate, such as in quasi-open spaces with only one limiting wall, and in wide channels, the motility behavior of bacteria with complex flagellar architectures approximately follows the hydrodynamics-based predictions developed for simple monotrichous bacteria. Specifically, V. natriegens and V. fischeri moved parallel to the wall and P. putida and E. coli presented a stable movement parallel to the wall but with incidental wall escape events, while M. marinus exhibited frequent flipping between wall accumulator and wall escaper regimes. Conversely, in tighter confining environments, the motility is governed by the steric interactions between bacteria and the surrounding walls. In mesoscale regions, where the impacts of hydrodynamics and steric interactions overlap, these mechanisms can either push bacteria in the same directions in linear channels, leading to smooth bacterial movement, or they could be oppositional (e.g., in mesoscale-sized meandered channels), leading to chaotic movement and subsequent bacterial trapping. The study provides a methodological template for the design of microfluidic devices for single-cell genomic screening, bacterial entrapment for diagnostics, or biocomputation.
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15
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Zhang Y, Krieger J, Mikulska-Ruminska K, Kaynak B, Sorzano COS, Carazo JM, Xing J, Bahar I. State-dependent sequential allostery exhibited by chaperonin TRiC/CCT revealed by network analysis of Cryo-EM maps. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 160:104-120. [PMID: 32866476 PMCID: PMC7914283 DOI: 10.1016/j.pbiomolbio.2020.08.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 06/25/2020] [Accepted: 08/16/2020] [Indexed: 12/17/2022]
Abstract
The eukaryotic chaperonin TRiC/CCT plays a major role in assisting the folding of many proteins through an ATP-driven allosteric cycle. Recent structures elucidated by cryo-electron microscopy provide a broad view of the conformations visited at various stages of the chaperonin cycle, including a sequential activation of its subunits in response to nucleotide binding. But we lack a thorough mechanistic understanding of the structure-based dynamics and communication properties that underlie the TRiC/CCT machinery. In this study, we present a computational methodology based on elastic network models adapted to cryo-EM density maps to gain a deeper understanding of the structure-encoded allosteric dynamics of this hexadecameric machine. We have analysed several structures of the chaperonin resolved in different states toward mapping its conformational landscape. Our study indicates that the overall architecture intrinsically favours cooperative movements that comply with the structural variabilities observed in experiments. Furthermore, the individual subunits CCT1-CCT8 exhibit state-dependent sequential events at different states of the allosteric cycle. For example, in the ATP-bound state, subunits CCT5 and CCT4 selectively initiate the lid closure motions favoured by the overall architecture; whereas in the apo form of the heteromer, the subunit CCT7 exhibits the highest predisposition to structural change. The changes then propagate through parallel fluxes of allosteric signals to neighbours on both rings. The predicted state-dependent mechanisms of sequential activation provide new insights into TRiC/CCT intra- and inter-ring signal transduction events.
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Affiliation(s)
- Yan Zhang
- Department of Computational and Systems Biology, University of Pittsburgh, 800 Murdoch Building, 3420 Forbes Avenue, Pittsburgh, PA, 15261, USA
| | - James Krieger
- Department of Computational and Systems Biology, University of Pittsburgh, 800 Murdoch Building, 3420 Forbes Avenue, Pittsburgh, PA, 15261, USA
| | - Karolina Mikulska-Ruminska
- Department of Computational and Systems Biology, University of Pittsburgh, 800 Murdoch Building, 3420 Forbes Avenue, Pittsburgh, PA, 15261, USA
| | - Burak Kaynak
- Department of Computational and Systems Biology, University of Pittsburgh, 800 Murdoch Building, 3420 Forbes Avenue, Pittsburgh, PA, 15261, USA
| | | | - José-María Carazo
- Centro Nacional de Biotecnología (CSIC), Darwin, 3, 28049, Madrid, Spain
| | - Jianhua Xing
- Department of Computational and Systems Biology, University of Pittsburgh, 800 Murdoch Building, 3420 Forbes Avenue, Pittsburgh, PA, 15261, USA
| | - Ivet Bahar
- Department of Computational and Systems Biology, University of Pittsburgh, 800 Murdoch Building, 3420 Forbes Avenue, Pittsburgh, PA, 15261, USA.
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16
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Afanzar O, Di Paolo D, Eisenstein M, Levi K, Plochowietz A, Kapanidis AN, Berry RM, Eisenbach M. The switching mechanism of the bacterial rotary motor combines tight regulation with inherent flexibility. EMBO J 2021; 40:e104683. [PMID: 33620739 PMCID: PMC7957414 DOI: 10.15252/embj.2020104683] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 12/17/2020] [Accepted: 01/19/2021] [Indexed: 11/20/2022] Open
Abstract
Regulatory switches are wide spread in many biological systems. Uniquely among them, the switch of the bacterial flagellar motor is not an on/off switch but rather controls the motor’s direction of rotation in response to binding of the signaling protein CheY. Despite its extensive study, the molecular mechanism underlying this switch has remained largely unclear. Here, we resolved the functions of each of the three CheY‐binding sites at the switch in E. coli, as well as their different dependencies on phosphorylation and acetylation of CheY. Based on this, we propose that CheY motor switching activity is potentiated upon binding to the first site. Binding of potentiated CheY to the second site produces unstable switching and at the same time enables CheY binding to the third site, an event that stabilizes the switched state. Thereby, this mechanism exemplifies a unique combination of tight motor regulation with inherent switching flexibility.
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Affiliation(s)
- Oshri Afanzar
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Diana Di Paolo
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK
| | - Miriam Eisenstein
- Department of Chemical Research Support, The Weizmann Institute of Science, Rehovot, Israel
| | - Kohava Levi
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Anne Plochowietz
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK
| | - Richard Michael Berry
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK
| | - Michael Eisenbach
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
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17
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Bell J, Araujo G, Tang JX. Discovery of oscillations in rotational speed of body-tethered Caulobacter crescentus. Phys Rev E 2021; 102:062416. [PMID: 33466088 DOI: 10.1103/physreve.102.062416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 11/09/2020] [Indexed: 11/07/2022]
Abstract
Swarmer cells of Caulobacter crescentus have been found to tether to glass at a point on the cell body. The rolling of the freely rotating flagellum near the glass surface causes the cell body to rotate. We describe the discovery of damped oscillations in the rotational speed of these cell bodies. We show that the damped oscillations are robust over multiple cells and that they depend more on the cell's accumulated rotation angle than on time. We also find that their phase is determined by the moment the flagellar motor changes the direction of its rotation. The oscillations occur only for one direction of cell rotation, when the flagellum is in pulling mode. We discuss possible explanations for these oscillations, including fluctuations in flagellar motor torque and periodic changes in flagellar orientation, and illustrate both of these cases using simplified computer models. Finally, we present the hypothesis that the oscillations are the result of fluctuations in the proton motive force, initiated by a sudden change in proton current that occurs when the motor switches rotation direction.
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Affiliation(s)
- Jordan Bell
- Department of Physics, Brown University, Providence, Rhode Island 02912, USA
| | - George Araujo
- Department of Physics, Brown University, Providence, Rhode Island 02912, USA
| | - Jay X Tang
- Department of Physics, Brown University, Providence, Rhode Island 02912, USA
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18
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Walker N, Tam KM. InfoCGAN classification of 2D square Ising configurations. MACHINE LEARNING: SCIENCE AND TECHNOLOGY 2021. [DOI: 10.1088/2632-2153/abcc45] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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19
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Structural Conservation and Adaptation of the Bacterial Flagella Motor. Biomolecules 2020; 10:biom10111492. [PMID: 33138111 PMCID: PMC7693769 DOI: 10.3390/biom10111492] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 02/07/2023] Open
Abstract
Many bacteria require flagella for the ability to move, survive, and cause infection. The flagellum is a complex nanomachine that has evolved to increase the fitness of each bacterium to diverse environments. Over several decades, molecular, biochemical, and structural insights into the flagella have led to a comprehensive understanding of the structure and function of this fascinating nanomachine. Notably, X-ray crystallography, cryo-electron microscopy (cryo-EM), and cryo-electron tomography (cryo-ET) have elucidated the flagella and their components to unprecedented resolution, gleaning insights into their structural conservation and adaptation. In this review, we focus on recent structural studies that have led to a mechanistic understanding of flagellar assembly, function, and evolution.
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20
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Dashti A, Mashayekhi G, Shekhar M, Ben Hail D, Salah S, Schwander P, des Georges A, Singharoy A, Frank J, Ourmazd A. Retrieving functional pathways of biomolecules from single-particle snapshots. Nat Commun 2020; 11:4734. [PMID: 32948759 PMCID: PMC7501871 DOI: 10.1038/s41467-020-18403-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 08/17/2020] [Indexed: 11/18/2022] Open
Abstract
A primary reason for the intense interest in structural biology is the fact that knowledge of structure can elucidate macromolecular functions in living organisms. Sustained effort has resulted in an impressive arsenal of tools for determining the static structures. But under physiological conditions, macromolecules undergo continuous conformational changes, a subset of which are functionally important. Techniques for capturing the continuous conformational changes underlying function are essential for further progress. Here, we present chemically-detailed conformational movies of biological function, extracted data-analytically from experimental single-particle cryo-electron microscopy (cryo-EM) snapshots of ryanodine receptor type 1 (RyR1), a calcium-activated calcium channel engaged in the binding of ligands. The functional motions differ substantially from those inferred from static structures in the nature of conformationally active structural domains, the sequence and extent of conformational motions, and the way allosteric signals are transduced within and between domains. Our approach highlights the importance of combining experiment, advanced data analysis, and molecular simulations.
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Affiliation(s)
- Ali Dashti
- Department of Physics, University of Wisconsin Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI, 53211, USA
| | - Ghoncheh Mashayekhi
- Department of Physics, University of Wisconsin Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI, 53211, USA
| | - Mrinal Shekhar
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign 405 N. Mathews Ave., Urbana, IL, 61801, USA
- School of Molecular Sciences, Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287, USA
| | - Danya Ben Hail
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, NY, 10031, USA
| | - Salah Salah
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, NY, 10031, USA
- Department of Chemistry & Biochemistry, City College of New York, New York, NY, 10031, USA
- Ph.D. Programs in Physics, Chemistry & Biochemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA
| | - Peter Schwander
- Department of Physics, University of Wisconsin Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI, 53211, USA
| | - Amedee des Georges
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, NY, 10031, USA.
- Department of Chemistry & Biochemistry, City College of New York, New York, NY, 10031, USA.
- Ph.D. Programs in Physics, Chemistry & Biochemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA.
| | - Abhishek Singharoy
- School of Molecular Sciences, Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287, USA.
| | - Joachim Frank
- Department of Biochemistry and Molecular Biophysics, Columbia University, 2-221 Black Building, 650 West 168th Street, New York, NY, 10032, USA.
- Department of Biological Sciences, Columbia University, 600 Fairchild Center, New York, NY, 10027, USA.
| | - Abbas Ourmazd
- Department of Physics, University of Wisconsin Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI, 53211, USA.
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21
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Walker N, Tam KM, Jarrell M. Deep learning on the 2-dimensional Ising model to extract the crossover region with a variational autoencoder. Sci Rep 2020; 10:13047. [PMID: 32747725 PMCID: PMC7400542 DOI: 10.1038/s41598-020-69848-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 07/06/2020] [Indexed: 11/10/2022] Open
Abstract
The 2-dimensional Ising model on a square lattice is investigated with a variational autoencoder in the non-vanishing field case for the purpose of extracting the crossover region between the ferromagnetic and paramagnetic phases. The encoded latent variable space is found to provide suitable metrics for tracking the order and disorder in the Ising configurations that extends to the extraction of a crossover region in a way that is consistent with expectations. The extracted results achieve an exceptional prediction for the critical point as well as agreement with previously published results on the configurational magnetizations of the model. The performance of this method provides encouragement for the use of machine learning to extract meaningful structural information from complex physical systems where little a priori data is available.
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Affiliation(s)
- Nicholas Walker
- Department of Physics and Astronomy, Louisiana State University, Baton Rouge, LA, 70803, USA.
| | - Ka-Ming Tam
- Department of Physics and Astronomy, Louisiana State University, Baton Rouge, LA, 70803, USA
- Center for Computation and Technology, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Mark Jarrell
- Department of Physics and Astronomy, Louisiana State University, Baton Rouge, LA, 70803, USA
- Center for Computation and Technology, Louisiana State University, Baton Rouge, LA, 70803, USA
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22
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Bacterial flagellar motor as a multimodal biosensor. Methods 2020; 193:5-15. [PMID: 32640316 DOI: 10.1016/j.ymeth.2020.06.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/04/2020] [Accepted: 06/22/2020] [Indexed: 01/05/2023] Open
Abstract
Bacterial Flagellar Motor is one of nature's rare rotary molecular machines. It enables bacterial swimming and it is the key part of the bacterial chemotactic network, one of the best studied chemical signalling networks in biology, which enables bacteria to direct its movement in accordance with the chemical environment. The network can sense down to nanomolar concentrations of specific chemicals on the time scale of seconds. Motor's rotational speed is linearly proportional to the electrochemical gradients of either proton or sodium driving ions, while its direction is regulated by the chemotactic network. Recently, it has been discovered that motor is also a mechanosensor. Given these properties, we discuss the motor's potential to serve as a multifunctional biosensor and a tool for characterising and studying the external environment, the bacterial physiology itself and single molecular motor biophysics.
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23
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Khan S. The Architectural Dynamics of the Bacterial Flagellar Motor Switch. Biomolecules 2020; 10:E833. [PMID: 32486003 PMCID: PMC7355467 DOI: 10.3390/biom10060833] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/23/2020] [Accepted: 05/25/2020] [Indexed: 02/06/2023] Open
Abstract
The rotary bacterial flagellar motor is remarkable in biochemistry for its highly synchronized operation and amplification during switching of rotation sense. The motor is part of the flagellar basal body, a complex multi-protein assembly. Sensory and energy transduction depends on a core of six proteins that are adapted in different species to adjust torque and produce diverse switches. Motor response to chemotactic and environmental stimuli is driven by interactions of the core with small signal proteins. The initial protein interactions are propagated across a multi-subunit cytoplasmic ring to switch torque. Torque reversal triggers structural transitions in the flagellar filament to change motile behavior. Subtle variations in the core components invert or block switch operation. The mechanics of the flagellar switch have been studied with multiple approaches, from protein dynamics to single molecule and cell biophysics. The architecture, driven by recent advances in electron cryo-microscopy, is available for several species. Computational methods have correlated structure with genetic and biochemical databases. The design principles underlying the basis of switch ultra-sensitivity and its dependence on motor torque remain elusive, but tantalizing clues have emerged. This review aims to consolidate recent knowledge into a unified platform that can inspire new research strategies.
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Affiliation(s)
- Shahid Khan
- Molecular Biology Consortium, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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24
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Abstract
Periplasmic flagella are complex nanomachines responsible for distinctive morphology and motility of spirochetes. Although bacterial flagella have been extensively studied for several decades in the model systems Escherichia coli and Salmonella enterica, our understanding of periplasmic flagella in many disease-causing spirochetes remains incomplete. Recent advances, including molecular genetics, biochemistry, structural biology, and cryo-electron tomography, have greatly increased our understanding of structure and function of periplasmic flagella. In this chapter, we summarize some of the recent findings that provide new insights into the structure, assembly, and function of periplasmic flagella.
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25
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High pressure inhibits signaling protein binding to the flagellar motor and bacterial chemotaxis through enhanced hydration. Sci Rep 2020; 10:2351. [PMID: 32047226 PMCID: PMC7012829 DOI: 10.1038/s41598-020-59172-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/27/2020] [Indexed: 12/13/2022] Open
Abstract
High pressure below 100 MPa interferes inter-molecular interactions without causing pressure denaturation of proteins. In Escherichia coli, the binding of the chemotaxis signaling protein CheY to the flagellar motor protein FliM induces reversal of the motor rotation. Using molecular dynamics (MD) simulations and parallel cascade selection MD (PaCS-MD), we show that high pressure increases the water density in the first hydration shell of CheY and considerably induces water penetration into the CheY-FliM interface. PaCS-MD enabled us to observe pressure-induced dissociation of the CheY-FliM complex at atomic resolution. Pressure dependence of binding free energy indicates that the increase of pressure from 0.1 to 100 MPa significantly weakens the binding. Using high-pressure microscopy, we observed that high hydrostatic pressure fixes the motor rotation to the counter-clockwise direction. In conclusion, the application of pressure enhances hydration of the proteins and weakens the binding of CheY to FliM, preventing reversal of the flagellar motor.
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26
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Nord AL, Pedaci F. Mechanisms and Dynamics of the Bacterial Flagellar Motor. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1267:81-100. [PMID: 32894478 DOI: 10.1007/978-3-030-46886-6_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Many bacteria are able to actively propel themselves through their complex environment, in search of resources and suitable niches. The source of this propulsion is the Bacterial Flagellar Motor (BFM), a molecular complex embedded in the bacterial membrane which rotates a flagellum. In this chapter we review the known physical mechanisms at work in the motor. The BFM shows a highly dynamic behavior in its power output, its structure, and in the stoichiometry of its components. Changes in speed, rotation direction, constituent protein conformations, and the number of constituent subunits are dynamically controlled in accordance to external chemical and mechanical cues. The mechano-sensitivity of the motor is likely related to the surface-sensing ability of bacteria, relevant in the initial stage of biofilm formation.
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Affiliation(s)
- A L Nord
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, University of Montpellier, Montpellier, France
| | - F Pedaci
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, University of Montpellier, Montpellier, France.
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27
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Lynch EM, Kollman JM. Coupled structural transitions enable highly cooperative regulation of human CTPS2 filaments. Nat Struct Mol Biol 2019; 27:42-48. [PMID: 31873303 PMCID: PMC6954954 DOI: 10.1038/s41594-019-0352-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 11/15/2019] [Indexed: 01/26/2023]
Abstract
Many enzymes assemble into defined oligomers, providing a mechanism for cooperatively regulating activity. Recent studies have described a mode of regulation in which enzyme activity is modulated by polymerization into large-scale filaments. Here we describe an ultrasensitive form of polymerization-based regulation employed by human CTP synthase 2 (CTPS2). Cryo-EM structures reveal that CTPS2 filaments dynamically switch between active and inactive forms in response to changes in substrate and product levels. Linking the conformational state of many CTPS2 subunits in a filament results in highly cooperative regulation, greatly exceeding the limits of cooperativity for the CTPS2 tetramer alone. The structures reveal a link between conformation and control of ammonia channeling between the enzyme’s active sites, and explain differences in regulation of human CTPS isoforms. This filament-based mechanism of enhanced cooperativity demonstrates how the widespread phenomenon of enzyme polymerization can be adapted to achieve different regulatory outcomes.
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Affiliation(s)
- Eric M Lynch
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Justin M Kollman
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
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28
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A General Workflow for Characterization of Nernstian Dyes and Their Effects on Bacterial Physiology. Biophys J 2019; 118:4-14. [PMID: 31810660 PMCID: PMC6950638 DOI: 10.1016/j.bpj.2019.10.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 10/08/2019] [Accepted: 10/18/2019] [Indexed: 12/22/2022] Open
Abstract
The electrical membrane potential (Vm) is one of the components of the electrochemical potential of protons across the biological membrane (proton motive force), which powers many vital cellular processes. Because Vm also plays a role in signal transduction, measuring it is of great interest. Over the years, a variety of techniques have been developed for the purpose. In bacteria, given their small size, Nernstian membrane voltage probes are arguably the favorite strategy, and their cytoplasmic accumulation depends on Vm according to the Nernst equation. However, a careful calibration of Nernstian probes that takes into account the tradeoffs between the ease with which the signal from the dye is observed and the dyes’ interactions with cellular physiology is rarely performed. Here, we use a mathematical model to understand such tradeoffs and apply the results to assess the applicability of the Thioflavin T dye as a Vm sensor in Escherichia coli. We identify the conditions in which the dye turns from a Vm probe into an actuator and, based on the model and experimental results, propose a general workflow for the characterization of Nernstian dye candidates.
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29
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Adaptive Responses of Shewanella decolorationis to Toxic Organic Extracellular Electron Acceptor Azo Dyes in Anaerobic Respiration. Appl Environ Microbiol 2019; 85:AEM.00550-19. [PMID: 31175185 DOI: 10.1128/aem.00550-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 05/29/2019] [Indexed: 12/18/2022] Open
Abstract
Bacterial anaerobic respiration using an extracellular electron acceptor plays a predominant role in global biogeochemical cycles. However, the mechanisms of bacterial adaptation to the toxic organic pollutant as the extracellular electron acceptor during anaerobic respiration are not clear, which limits our ability to optimize the strategies for the bioremediation of a contaminated environment. Here, we report the physiological characteristics and the global gene expression of an ecologically successful bacterium, Shewanella decolorationis S12, when using a typical toxic organic pollutant, amaranth, as the extracellular electron acceptor. Our results revealed that filamentous shift (the cells stretched to fiber-like shapes as long as 18 μm) occurred under amaranth stress. Persistent stress led to a higher filamentous cell rate and decolorization ability in subcultural cells compared to parental strains. In addition, the expression of genes involved in cell division, the chemotaxis system, energy conservation, damage repair, and material transport in filamentous cells was significantly stimulated. The detailed roles of some genes with significantly elevated expressions in filamentous cells, such as the outer membrane porin genes ompA and ompW, the cytochrome c genes arpC and arpD, the global regulatory factor gene rpoS, and the methyl-accepting chemotaxis proteins genes SHD_2793 and SHD_0015, were identified by site-directed mutagenesis. Finally, a conceptual model was proposed to help deepen our insights into both the bacterial survival strategy when toxic organics were present and the mechanisms by which these toxic organics were biodegraded as the extracellular electron acceptors.IMPORTANCE Keeping toxic organic pollutants (TOPs) in tolerable levels is a huge challenge for bacteria in extremely unfavorable environments since TOPs could serve as energy substitutes but also as survival stresses when they are beyond some thresholds. This study focused on the underlying adaptive mechanisms of ecologically successful bacterium Shewanella decolorationis S12 when exposed to amaranth, a typical toxic organic pollutant, as the extracellular electron acceptor. Our results suggest that filamentous shift is a flexible and valid way to solve the dilemma between the energy resource and toxic stress. Filamentous cells regulate gene expression to enhance their degradation and detoxification capabilities, resulting in a strong viability. These novel adaptive responses to TOPs are believed to be an evolutionary achievement to succeed in harsh habitats and thus have great potential to be applied to environment engineering or synthetic biology if we could picture every unknown node in this pathway.
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Minamino T, Kinoshita M, Namba K. Directional Switching Mechanism of the Bacterial Flagellar Motor. Comput Struct Biotechnol J 2019; 17:1075-1081. [PMID: 31452860 PMCID: PMC6700473 DOI: 10.1016/j.csbj.2019.07.020] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/26/2019] [Accepted: 07/27/2019] [Indexed: 11/16/2022] Open
Abstract
Bacteria sense temporal changes in extracellular stimuli via sensory signal transducers and move by rotating flagella towards into a favorable environment for their survival. Each flagellum is a supramolecular motility machine consisting of a bi-directional rotary motor, a universal joint and a helical propeller. The signal transducers transmit environmental signals to the flagellar motor through a cytoplasmic chemotactic signaling pathway. The flagellar motor is composed of a rotor and multiple stator units, each of which acts as a transmembrane proton channel to conduct protons and exert force on the rotor. FliG, FliM and FliN form the C ring on the cytoplasmic face of the basal body MS ring made of the transmembrane protein FliF and act as the rotor. The C ring also serves as a switching device that enables the motor to spin in both counterclockwise (CCW) and clockwise (CW) directions. The phosphorylated form of the chemotactic signaling protein CheY binds to FliM and FliN to induce conformational changes of the C ring responsible for switching the direction of flagellar motor rotation from CCW to CW. In this mini-review, we will describe current understanding of the switching mechanism of the bacterial flagellar motor.
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Affiliation(s)
- Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadoaka, Suita, Osaka 565-0871, Japan
| | - Miki Kinoshita
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadoaka, Suita, Osaka 565-0871, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadoaka, Suita, Osaka 565-0871, Japan
- RIKEN Center for Biosystems Dynamic Research & Spring-8 Center, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
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31
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Flagella-Driven Motility of Bacteria. Biomolecules 2019; 9:biom9070279. [PMID: 31337100 PMCID: PMC6680979 DOI: 10.3390/biom9070279] [Citation(s) in RCA: 174] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/11/2019] [Accepted: 07/12/2019] [Indexed: 01/17/2023] Open
Abstract
The bacterial flagellum is a helical filamentous organelle responsible for motility. In bacterial species possessing flagella at the cell exterior, the long helical flagellar filament acts as a molecular screw to generate thrust. Meanwhile, the flagella of spirochetes reside within the periplasmic space and not only act as a cytoskeleton to determine the helicity of the cell body, but also rotate or undulate the helical cell body for propulsion. Despite structural diversity of the flagella among bacterial species, flagellated bacteria share a common rotary nanomachine, namely the flagellar motor, which is located at the base of the filament. The flagellar motor is composed of a rotor ring complex and multiple transmembrane stator units and converts the ion flux through an ion channel of each stator unit into the mechanical work required for motor rotation. Intracellular chemotactic signaling pathways regulate the direction of flagella-driven motility in response to changes in the environments, allowing bacteria to migrate towards more desirable environments for their survival. Recent experimental and theoretical studies have been deepening our understanding of the molecular mechanisms of the flagellar motor. In this review article, we describe the current understanding of the structure and dynamics of the bacterial flagellum.
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Krasnopeeva E, Lo CJ, Pilizota T. Single-Cell Bacterial Electrophysiology Reveals Mechanisms of Stress-Induced Damage. Biophys J 2019; 116:2390-2399. [PMID: 31174851 PMCID: PMC6588726 DOI: 10.1016/j.bpj.2019.04.039] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 04/06/2019] [Accepted: 04/17/2019] [Indexed: 01/01/2023] Open
Abstract
An electrochemical gradient of protons, or proton motive force (PMF), is at the basis of bacterial energetics. It powers vital cellular processes and defines the physiological state of the cell. Here, we use an electric circuit analogy of an Escherichia coli cell to mathematically describe the relationship between bacterial PMF, electric properties of the cell membrane, and catabolism. We combine the analogy with the use of bacterial flagellar motor as a single-cell "voltmeter" to measure cellular PMF in varied and dynamic external environments (for example, under different stresses). We find that butanol acts as an ionophore and functionally characterize membrane damage caused by the light of shorter wavelengths. Our approach coalesces noninvasive and fast single-cell voltmeter with a well-defined mathematical framework to enable quantitative bacterial electrophysiology.
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Affiliation(s)
- Ekaterina Krasnopeeva
- Centre for Synthetic and Systems Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Chien-Jung Lo
- Department of Physics and Graduate Institute of Biophysics, National Central University, Jhongli, Taiwan, Republic of China
| | - Teuta Pilizota
- Centre for Synthetic and Systems Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom.
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33
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Roth J, Koch MD, Rohrbach A. Dynamics of a Protein Chain Motor Driving Helical Bacteria under Stress. Biophys J 2019; 114:1955-1969. [PMID: 29694872 DOI: 10.1016/j.bpj.2018.02.043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 02/27/2018] [Accepted: 02/28/2018] [Indexed: 12/21/2022] Open
Abstract
The wall-less, helical bacterial genus Spiroplasma has a unique propulsion system; it is not driven by propeller-like flagella but by a membrane-bound, cytoplasmic, linear motor that consists of a contractile chain of identical proteins spanning the entire cell length. By a coordinated spread of conformational changes of the proteins, kinks propagate in pairs along the cell body. However, the mechanisms for the initiation or delay of kinks and their coordinated spread remain unclear. Here, we show how we manipulate the initiation of kinks, their propagation velocities, and the time between two kinks for a single cell trapped in an optical line potential. By interferometric three-dimensional shape tracking, we measured the cells' deformations in response to various external stress situations. We observed a significant dependency of force generation on the cells' local ligand concentrations (likely ATP) and ligand hydrolysis, which we altered in different ways. We developed a mechanistic, mathematical model based on Kramer's rates, describing the subsequent cooperative and conformational switching of the chain's proteins. The model reproduces our experimental observations and can explain deformation characteristics even when the motor is driven to its extreme. Nature has invented a set of minimalistic mechanical driving concepts. To understand or even rebuild them, it is essential to reveal the molecular mechanisms of such protein chain motors, which need only two components-coupled proteins and ligands-to function.
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Affiliation(s)
- Julian Roth
- Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany
| | - Matthias D Koch
- Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany; Princeton University, Princeton, New Jersey
| | - Alexander Rohrbach
- Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany.
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34
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Recent Advances in Computational Protocols Addressing Intrinsically Disordered Proteins. Biomolecules 2019; 9:biom9040146. [PMID: 30979035 PMCID: PMC6523529 DOI: 10.3390/biom9040146] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 01/09/2023] Open
Abstract
Intrinsically disordered proteins (IDP) are abundant in the human genome and have recently emerged as major therapeutic targets for various diseases. Unlike traditional proteins that adopt a definitive structure, IDPs in free solution are disordered and exist as an ensemble of conformations. This enables the IDPs to signal through multiple signaling pathways and serve as scaffolds for multi-protein complexes. The challenge in studying IDPs experimentally stems from their disordered nature. Nuclear magnetic resonance (NMR), circular dichroism, small angle X-ray scattering, and single molecule Förster resonance energy transfer (FRET) can give the local structural information and overall dimension of IDPs, but seldom provide a unified picture of the whole protein. To understand the conformational dynamics of IDPs and how their structural ensembles recognize multiple binding partners and small molecule inhibitors, knowledge-based and physics-based sampling techniques are utilized in-silico, guided by experimental structural data. However, efficient sampling of the IDP conformational ensemble requires traversing the numerous degrees of freedom in the IDP energy landscape, as well as force-fields that accurately model the protein and solvent interactions. In this review, we have provided an overview of the current state of computational methods for studying IDP structure and dynamics and discussed the major challenges faced in this field.
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35
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Mukherjee T, Elmas M, Vo L, Alexiades V, Hong T, Alexandre G. Multiple CheY Homologs Control Swimming Reversals and Transient Pauses in Azospirillum brasilense. Biophys J 2019; 116:1527-1537. [PMID: 30975454 DOI: 10.1016/j.bpj.2019.03.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 02/26/2019] [Accepted: 03/13/2019] [Indexed: 12/11/2022] Open
Abstract
Chemotaxis, together with motility, helps bacteria foraging in their habitat. Motile bacteria exhibit a variety of motility patterns, often controlled by chemotaxis, to promote dispersal. Motility in many bacteria is powered by a bidirectional flagellar motor. The flagellar motor has been known to briefly pause during rotation because of incomplete reversals or stator detachment. Transient pauses were previously observed in bacterial strains lacking CheY, and these events could not be explained by incomplete motor reversals or stator detachment. Here, we systematically analyzed swimming trajectories of various chemotaxis mutants of the monotrichous soil bacterium, Azospirillum brasilense. Like other polar flagellated bacterium, the main swimming pattern in A. brasilense is run and reverse. A. brasilense also uses run-pauses and putative run-reverse-flick-like swimming patterns, although these are rare events. A. brasilense mutant derivatives lacking the chemotaxis master histidine kinase, CheA4, or the central response regulator, CheY7, also showed transient pauses. Strikingly, the frequency of transient pauses increased dramatically in the absence of CheY4. Our findings collectively suggest that reversals and pauses are controlled through signaling by distinct CheY homologs, and thus are likely to be functionally important in the lifestyle of this soil organism.
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Affiliation(s)
- Tanmoy Mukherjee
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee
| | - Mustafa Elmas
- Department of Mathematics, University of Tennessee, Knoxville, Tennessee
| | - Lam Vo
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee
| | - Vasilios Alexiades
- Department of Mathematics, University of Tennessee, Knoxville, Tennessee
| | - Tian Hong
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee; National Institute for Mathematical and Biological Synthesis, University of Tennessee, Knoxville, Tennessee
| | - Gladys Alexandre
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee.
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36
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Bacterial flagellar switching: a molecular mechanism directed by the logic of an electric motor. J Mol Model 2018; 24:280. [DOI: 10.1007/s00894-018-3819-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 08/30/2018] [Indexed: 11/27/2022]
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37
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Cominetti O, Smith D, Hoffman F, Jallow M, Thézénas ML, Huang H, Kwiatkowski D, Maini PK, Casals-Pascual C. Identification of a Novel Clinical Phenotype of Severe Malaria using a Network-Based Clustering Approach. Sci Rep 2018; 8:12849. [PMID: 30150696 PMCID: PMC6110866 DOI: 10.1038/s41598-018-31320-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 08/14/2018] [Indexed: 11/29/2022] Open
Abstract
The parasite Plasmodium falciparum is the main cause of severe malaria (SM). Despite treatment with antimalarial drugs, more than 400,000 deaths are reported every year, mainly in African children. The diversity of clinical presentations associated with SM highlights important differences in disease pathogenesis that often require specific therapeutic options. The clinical heterogeneity of SM is largely unresolved. Here we report a network-based analysis of clinical phenotypes associated with SM in 2,915 Gambian children admitted to hospital with Plasmodium falciparum malaria. We used a network-based clustering method which revealed a strong correlation between disease heterogeneity and mortality. The analysis identified four distinct clusters of SM and respiratory distress that departed from the WHO definition. Patients in these clusters characteristically presented with liver enlargement and high concentrations of brain natriuretic peptide (BNP), giving support to the potential role of circulatory overload and/or right-sided heart failure as a mechanism of disease. The role of heart failure is controversial in SM and our work suggests that standard clinical management may not be appropriate. We find that our clustering can be a powerful data exploration tool to identify novel disease phenotypes and therapeutic options to reduce malaria-associated mortality.
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Affiliation(s)
- Ornella Cominetti
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, UK
- Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - David Smith
- London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - Fred Hoffman
- Department of Computer Science, University of Oxford, Oxford, UK
- XL Catlin, London, UK
| | | | - Marie L Thézénas
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Honglei Huang
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Philip K Maini
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, UK
| | - Climent Casals-Pascual
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
- ISGlobal, Hospital Clínic i Provincial de Barcelona, Centre Diagnòstic Biomèdic- Universitat de Barcelona, Barcelona, Spain.
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38
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Khan S, Guo TW, Misra S. A coevolution-guided model for the rotor of the bacterial flagellar motor. Sci Rep 2018; 8:11754. [PMID: 30082903 PMCID: PMC6079021 DOI: 10.1038/s41598-018-30293-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/19/2018] [Indexed: 01/17/2023] Open
Abstract
The Salmonella typhimurium trans-membrane FliF MS ring templates assembly of the rotary bacterial flagellar motor, which also contains a cytoplasmic C-ring. A full-frame fusion of FliF with the rotor protein FliG assembles rings in non-motile expression hosts. 3D electron microscopy reconstructions of these FliFFliG rings show three high electron-density sub-volumes. 3D-classification revealed heterogeneity of the assigned cytoplasmic volume consistent with FliG lability. We used residue coevolution to construct homodimer building blocks for ring assembly, with X-ray crystal structures from other species and injectisome analogs. The coevolution signal validates folds and, importantly, indicates strong homodimer contacts for three ring building motifs (RBMs), initially identified in injectisome structures. It also indicates that the cofolded domains of the FliG N-terminal domain (FliG_N) with embedded α-helical FliF carboxy-terminal tail homo-oligomerize. The FliG middle and C-terminal domains (FliG_MC) have a weak signal for homo-dimerization but have coevolved to conserve their stacking contact. The homodimers and their ring models fit well into the 3D reconstruction. We hypothesize that a stable FliF periplasmic hub provides a platform for FliG ring self-assembly, but the FliG_MC ring has only limited stability without the C-ring. We also present a mechanical model for torque transmission in the FliFFliG ring.
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Affiliation(s)
- Shahid Khan
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
- Molecular Biology Consortium, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Tai Wei Guo
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Saurav Misra
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
- Department of Biochemistry & Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
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39
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dos Santos RN, Khan S, Morcos F. Characterization of C-ring component assembly in flagellar motors from amino acid coevolution. ROYAL SOCIETY OPEN SCIENCE 2018; 5:171854. [PMID: 29892378 PMCID: PMC5990795 DOI: 10.1098/rsos.171854] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 04/05/2018] [Indexed: 06/08/2023]
Abstract
Bacterial flagellar motility, an important virulence factor, is energized by a rotary motor localized within the flagellar basal body. The rotor module consists of a large framework (the C-ring), composed of the FliG, FliM and FliN proteins. FliN and FliM contacts the FliG torque ring to control the direction of flagellar rotation. We report that structure-based models constrained only by residue coevolution can recover the binding interface of atomic X-ray dimer complexes with remarkable accuracy (approx. 1 Å RMSD). We propose a model for FliM-FliN heterodimerization, which agrees accurately with homologous interfaces as well as in situ cross-linking experiments, and hence supports a proposed architecture for the lower portion of the C-ring. Furthermore, this approach allowed the identification of two discrete and interchangeable homodimerization interfaces between FliM middle domains that agree with experimental measurements and might be associated with C-ring directional switching dynamics triggered upon binding of CheY signal protein. Our findings provide structural details of complex formation at the C-ring that have been difficult to obtain with previous methodologies and clarify the architectural principle that underpins the ultra-sensitive allostery exhibited by this ring assembly that controls the clockwise or counterclockwise rotation of flagella.
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Affiliation(s)
- Ricardo Nascimento dos Santos
- Institute of Chemistry and Center for Computational Engineering and Science, University of Campinas, Campinas, SP, Brazil
| | - Shahid Khan
- Molecular Biology Consortium, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Faruck Morcos
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX, USA
- Department of Bioengineering, University of Texas at Dallas, Richardson, TX, USA
- Center for Systems Biology, University of Texas at Dallas, Richardson, TX, USA
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40
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Waite AJ, Frankel NW, Emonet T. Behavioral Variability and Phenotypic Diversity in Bacterial Chemotaxis. Annu Rev Biophys 2018; 47:595-616. [PMID: 29618219 DOI: 10.1146/annurev-biophys-062215-010954] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Living cells detect and process external signals using signaling pathways that are affected by random fluctuations. These variations cause the behavior of individual cells to fluctuate over time (behavioral variability) and generate phenotypic differences between genetically identical individuals (phenotypic diversity). These two noise sources reduce our ability to predict biological behavior because they diversify cellular responses to identical signals. Here, we review recent experimental and theoretical advances in understanding the mechanistic origin and functional consequences of such variation in Escherichia coli chemotaxis-a well-understood model of signal transduction and behavior. After briefly summarizing the architecture and logic of the chemotaxis system, we discuss determinants of behavior and chemotactic performance of individual cells. Then, we review how cell-to-cell differences in protein abundance map onto differences in individual chemotactic abilities and how phenotypic variability affects the performance of the population. We conclude with open questions to be addressed by future research.
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Affiliation(s)
- Adam James Waite
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520; .,Current affiliation: Calico Life Sciences, LLC, South San Francisco, California 94080
| | - Nicholas W Frankel
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520; .,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158
| | - Thierry Emonet
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520; .,Department of Physics, Yale University, New Haven, Connecticut 06520
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41
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Onoue Y, Takekawa N, Nishikino T, Kojima S, Homma M. The role of conserved charged residues in the bidirectional rotation of the bacterial flagellar motor. Microbiologyopen 2018; 7:e00587. [PMID: 29573373 PMCID: PMC6079164 DOI: 10.1002/mbo3.587] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 12/19/2017] [Accepted: 12/28/2017] [Indexed: 12/23/2022] Open
Abstract
Many bacteria rotate their flagella both counterclockwise (CCW) and clockwise (CW) to achieve swimming toward attractants or away from repellents. Highly conserved charged residues are important for that motility, which suggests that electrostatic interactions are crucial for the rotor-stator function. It remains unclear if those residues contribute equally to rotation in the CCW and CW directions. To address this uncertainty, in this study, we expressed chimeric rotors and stators from Vibrio alginolyticus and Escherichia coli in E. coli, and measured the rotational speed of each motor in both directions using a tethered-cell assay. In wild-type cells, the rotational speeds in both directions were equal, as demonstrated previously. Some charge-neutralizing residue replacements in the stator decreased the rotational speed in both directions to the same extent. However, mutations in two charged residues in the rotor decreased the rotational speed only in the CCW direction. Subsequent analysis and previous results suggest that these amino acid residues are involved in supporting the conformation of the rotor, which is important for proper torque generation in the CCW direction.
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Affiliation(s)
- Yasuhiro Onoue
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Norihiro Takekawa
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Tatsuro Nishikino
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Seiji Kojima
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Michio Homma
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
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42
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Quantitative Modeling of Flagellar Motor-Mediated Adaptation. Methods Mol Biol 2018. [PMID: 29429103 DOI: 10.1007/978-1-4939-7577-8_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The bacterial flagellar motor is capable of adapting to changes in the concentrations of extracellular chemical stimuli by changing the composition of the switch complex of the flagellar motor. Such remodeling-based adaptation complements the receptor-mediated adaptation in the chemotaxis network to help maintain high sensitivity in the response of the motor to phospho-CheY concentrations, despite cell-to-cell variability in the abundances of chemotaxis proteins. In this chapter, a modeling approach is described that explains the mechanisms of switch-remodeling and motor-mediated adaptation. The approach is based on observations of structural differences, associated with the direction of motor rotation, that modulate the strength of FliM/FliN binding within the switch. By modulating the number of CheY-P-binding sites within the motor, remodeling maximizes sensitivity over a range of signal levels.
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43
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Kinoshita M, Furukawa Y, Uchiyama S, Imada K, Namba K, Minamino T. Insight into adaptive remodeling of the rotor ring complex of the bacterial flagellar motor. Biochem Biophys Res Commun 2017; 496:12-17. [PMID: 29294326 DOI: 10.1016/j.bbrc.2017.12.118] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 12/04/2017] [Accepted: 12/20/2017] [Indexed: 12/23/2022]
Abstract
The bacterial flagellar motor rotates in both counterclockwise (CCW) and clockwise (CW) directions. FliG, FliM and FliN form the C ring on the cytoplasmic face of the MS ring made of a transmembrane protein, FliF. The C ring acts not only as a rotor but also as a switch of the direction of motor rotation. FliG consists of three domains: FliGN, FliGM and FliGC. FliGN directly binds to FliF. Intermolecular interactions between FliGM and FliGC drive FliG ring formation. FliGM is responsible for the interaction with FliM. FliGC is involved in the interaction with the stator protein MotA. Adaptive remodeling of the C ring occurs when the motor switches between the CCW and CW states. However, it remained unknown how. Here, we report the effects of a CW-locked deletion mutation (ΔPEV) in FliG of Thermotaoga maritia (Tm-FliG) on FliG-FliG and FliG-FliM interactions. The PEV deletion stabilized the intramolecular interaction between FliGM and FliGC, thereby suppressing the oligomerization of Tm-FliGMC in solution. This deletion also induced a conformational change of HelixMC connecting FliGM and FliGC to reduce the binding affinity of Tm-FliGMC for FliM. We will discuss adaptive remodeling of the C ring responsible for flagellar motor switching.
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Affiliation(s)
- Miki Kinoshita
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadoaka, Suita, Osaka 565-0871, Japan
| | - Yukio Furukawa
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadoaka, Suita, Osaka 565-0871, Japan
| | - Susumu Uchiyama
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Katsumi Imada
- Department of Macromolecular Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadoaka, Suita, Osaka 565-0871, Japan; Quantitative Biology Center, RIKEN, 1-3 Yamadoaka, Suita, Osaka 565-0871, Japan
| | - Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadoaka, Suita, Osaka 565-0871, Japan.
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44
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Keegstra JM, Kamino K, Anquez F, Lazova MD, Emonet T, Shimizu TS. Phenotypic diversity and temporal variability in a bacterial signaling network revealed by single-cell FRET. eLife 2017; 6:27455. [PMID: 29231170 PMCID: PMC5809149 DOI: 10.7554/elife.27455] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 11/17/2017] [Indexed: 11/13/2022] Open
Abstract
We present in vivo single-cell FRET measurements in the Escherichia coli chemotaxis system that reveal pervasive signaling variability, both across cells in isogenic populations and within individual cells over time. We quantify cell-to-cell variability of adaptation, ligand response, as well as steady-state output level, and analyze the role of network design in shaping this diversity from gene expression noise. In the absence of changes in gene expression, we find that single cells demonstrate strong temporal fluctuations. We provide evidence that such signaling noise can arise from at least two sources: (i) stochastic activities of adaptation enzymes, and (ii) receptor-kinase dynamics in the absence of adaptation. We demonstrate that under certain conditions, (ii) can generate giant fluctuations that drive signaling activity of the entire cell into a stochastic two-state switching regime. Our findings underscore the importance of molecular noise, arising not only in gene expression but also in protein networks. Many sophisticated computer programs use random number generators to help solve challenging problems. These problems range from achieving secure communication across the Internet to deciding how best to invest in the stock market. Much research in recent years has found that randomness is also widespread in living cells, where it is often called “noise”. For example, the activity of some genes is so unpredictable to the extent that it appears random. Yet, relatively little is known about how such gene-expression noise propagates up to change how the cell behaves. Many open questions also remain about how cells might exploit these or other fluctuations to achieve complex tasks, like people use random number generators. Bacteria perform a number of complex tasks. Some bacteria will swim toward chemicals that suggest a potential reward, such as food. Yet they swim away from chemicals that could lead them to harm. This ability is called chemotaxis and it relies on a network of interacting enzymes and other proteins that coordinates a bacterium’s movements with the input from its senses. Keegstra et al. set out to find sources of noise that might act as random number generators and help the bacterium E. coli to best perform chemotaxis. An improved version of a technique called in vivo Förster resonance energy transfer (or in vivo FRET for short) was used to give a detectable signal when two proteins involved in the chemotaxis network interacted inside a single bacterium. The experiments showed that this protein network amplifies gene-expression noise for some genes while lessening it for others. In addition, the interactions between proteins encoded by genes acted as an extra source of noise, even when gene-expression noise was eliminated. Keegstra et al. found that the amount of signaling within the chemotaxis network, as measured by in vivo FRET, varied wildly over time. This revealed two sources of noise at the level of protein signaling. One was due to randomness in the activity of the enzymes involved in tuning the cell’s sensitivity to changes in its environment. The other was due to protein interactions within a large complex that acts as the cell’s sensor. Unexpectedly, this second source of noise under some conditions could be so strong that it flipped the output of the cell’s signaling network back and forth between just two states: “on” and “off”. Together these findings uncover how signaling networks can not only amplify or lessen gene-expression noise, but can themselves become a source of random events. The new knowledge of how such random events interact with a complex trait in a living cell – namely chemotaxis – could aid future antimicrobial strategies, because many bacteria use chemotaxis to help them establish infections. More generally, the new insights about noise in protein networks could help engineers seeking to build synthetic biochemical networks or produce useful compounds in living cells.
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Affiliation(s)
| | | | | | | | - Thierry Emonet
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States.,Department of Physics, Yale University, New Haven, United States
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45
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Impact of fluorescent protein fusions on the bacterial flagellar motor. Sci Rep 2017; 7:12583. [PMID: 28974721 PMCID: PMC5626733 DOI: 10.1038/s41598-017-11241-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 08/22/2017] [Indexed: 01/16/2023] Open
Abstract
Fluorescent fusion proteins open a direct and unique window onto protein function. However, they also introduce the risk of perturbation of the function of the native protein. Successful applications of fluorescent fusions therefore rely on a careful assessment and minimization of the side effects, but such insight is still lacking for many applications. This is particularly relevant in the study of the internal dynamics of motor proteins, where both the chemical and mechanical reaction coordinates can be affected. Fluorescent proteins fused to the stator of the Bacterial Flagellar Motor (BFM) have previously been used to unveil the motor subunit dynamics. Here we report the effects on single motors of three fluorescent proteins fused to the stators, all of which altered BFM behavior. The torque generated by individual stators was reduced while their stoichiometry remained unaffected. MotB fusions decreased the switching frequency and induced a novel bias-dependent asymmetry in the speed in the two directions. These effects could be mitigated by inserting a linker at the fusion point. These findings provide a quantitative account of the effects of fluorescent fusions to the stator on BFM dynamics and their alleviation- new insights that advance the use of fluorescent fusions to probe the dynamics of protein complexes.
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46
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Pourjaberi SNS, Terahara N, Namba K, Minamino T. The role of a cytoplasmic loop of MotA in load-dependent assembly and disassembly dynamics of the MotA/B stator complex in the bacterial flagellar motor. Mol Microbiol 2017; 106:646-658. [DOI: 10.1111/mmi.13843] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/18/2017] [Indexed: 11/26/2022]
Affiliation(s)
| | - Naoya Terahara
- Graduate School of Frontier Biosciences; Osaka University, 1-3 Yamadaoka; Suita Osaka 565-0871 Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences; Osaka University, 1-3 Yamadaoka; Suita Osaka 565-0871 Japan
- RIKEN; Quantitative Biology Center, 1-3 Yamadaoka; Suita Osaka 565-0871 Japan
| | - Tohru Minamino
- Graduate School of Frontier Biosciences; Osaka University, 1-3 Yamadaoka; Suita Osaka 565-0871 Japan
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47
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Abstract
Bacterial motility, and in particular repulsion or attraction toward specific chemicals, has been a subject of investigation for over 100 years, resulting in detailed understanding of bacterial chemotaxis and the corresponding sensory network in many bacterial species. For Escherichia coli most of the current understanding comes from the experiments with low levels of chemotactically active ligands. However, chemotactically inactive chemical species at concentrations found in the human gastrointestinal tract produce significant changes in E. coli's osmotic pressure and have been shown to lead to taxis. To understand how these nonspecific physical signals influence motility, we look at the response of individual bacterial flagellar motors under stepwise changes in external osmolarity. We combine these measurements with a population swimming assay under the same conditions. Unlike for chemotactic response, a long-term increase in swimming/motor speeds is observed, and in the motor rotational bias, both of which scale with the osmotic shock magnitude. We discuss how the speed changes we observe can lead to steady-state bacterial accumulation.
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48
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Colin R, Sourjik V. Emergent properties of bacterial chemotaxis pathway. Curr Opin Microbiol 2017; 39:24-33. [PMID: 28822274 DOI: 10.1016/j.mib.2017.07.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Accepted: 07/27/2017] [Indexed: 11/17/2022]
Abstract
The chemotaxis pathway of Escherichia coli is the most studied sensory system in prokaryotes. The highly conserved general architecture of this pathway consists of two modules which mediate signal transduction and adaptation. The signal transduction module detects and amplifies changes in environmental conditions and rapidly transmits these signals to control bacterial swimming behavior. The adaptation module gradually resets the activity and sensitivity of the first module after initial stimulation and thereby enables the temporal comparisons necessary for bacterial chemotaxis. Recent experimental and theoretical work has unraveled multiple quantitative features emerging from the interplay between these two modules. This has laid the groundwork for rationalization of these emerging properties in the context of the evolutionary optimization of the chemotactic behavior.
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Affiliation(s)
- Remy Colin
- Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology, Karl-von-Frisch-strasse 16, 35043 Marburg, Germany
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology, Karl-von-Frisch-strasse 16, 35043 Marburg, Germany.
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49
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Nirody JA, Berry RM, Oster G. The Limiting Speed of the Bacterial Flagellar Motor. Biophys J 2017; 111:557-564. [PMID: 27508439 DOI: 10.1016/j.bpj.2016.07.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 06/13/2016] [Accepted: 07/05/2016] [Indexed: 12/21/2022] Open
Abstract
Recent experiments on the bacterial flagellar motor have shown that the structure of this nanomachine, which drives locomotion in a wide range of bacterial species, is more dynamic than previously believed. Specifically, the number of active torque-generating complexes (stators) was shown to vary across applied loads. This finding brings under scrutiny the experimental evidence reporting that limiting (zero-torque) speed is independent of the number of active stators. In this study, we propose that, contrary to previous assumptions, the maximum speed of the motor increases as additional stators are recruited. This result arises from our assumption that stators disengage from the motor for a significant portion of their mechanochemical cycles at low loads. We show that this assumption is consistent with current experimental evidence in chimeric motors, as well as with the requirement that a processive motor driving a large load via an elastic linkage must have a high duty ratio.
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Affiliation(s)
- Jasmine A Nirody
- Biophysics Graduate Group, University of California, Berkeley, Berkeley, California.
| | - Richard M Berry
- Department of Physics, Clarendon Laboratory, University of Oxford, United Kingdom
| | - George Oster
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California
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50
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Nakauma A, van Doorn GS. Reconstructing the genotype-to-fitness map for the bacterial chemotaxis network and its emergent behavioural phenotypes. J Theor Biol 2017; 420:200-212. [PMID: 28322874 DOI: 10.1016/j.jtbi.2017.03.016] [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: 11/22/2016] [Revised: 02/10/2017] [Accepted: 03/16/2017] [Indexed: 11/26/2022]
Abstract
The signal-transduction network responsible for chemotaxis in Escherichia coli has been characterised in extraordinary detail. Yet, relatively little is known about eco-evolutionary aspects of chemotaxis, such as how the network has been shaped by selection and to what extent natural populations may fine-tune their chemotactic behaviour to the ecological conditions. To address these questions, we here develop an evolutionary-systems-biology model of the chemotaxis network of E. coli, which we apply to estimate the resource accumulation rate (here used as a proxy for fitness) of wildtype and a large number of potential mutant genotypes. Mutant genotypes differ from the wildtype in the concentrations of one or more constituent proteins of the chemotaxis signalling network or in one or more of its kinetic parameters. To guarantee model consistency across the genotype space, we explicitly incorporated biochemical constraints that underly observed phenotypic trade-offs. The model was validated by reconstructing the phenotypic properties of several known mutant genotypes. We also characterised differences in the fitness distribution between genotypes, and reconstructed adaptive walks in genotype space for populations exposed to different environmental conditions. We found that the local fitness landscape is rugged, due to non-additive interactions between mutations. When selection has a consistent direction, just a few adaptive mutations are required to reach a local peak, and different local peaks can be reached by adaptive walks starting from the same initial genotype. However, when the direction of selection is fluctuating, evolutionary paths are much longer and genotype space is explored further. Longer adaptive walks were also observed when evolution was started from a low-fitness genotype such as a CheZ knockout mutant. In line with empirical observations, the initial ΔcheZ mutant did not respond to a step-down stimulus, but a dynamic response similar to the wildtype was recovered following the fixation of compensatory mutations.
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Affiliation(s)
- Alberto Nakauma
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9700 CC Groningen, The Netherlands.
| | - G Sander van Doorn
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9700 CC Groningen, The Netherlands
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