1
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Jünger F, Rohrbach A. Making Hidden Cell Particle Interactions Visible by Thermal Noise Frequency Decomposition. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2207032. [PMID: 37337392 DOI: 10.1002/smll.202207032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 02/15/2023] [Indexed: 06/21/2023]
Abstract
Thermal noise drives cellular structures, bacteria, and viruses on different temporal and spatial scales. Their weak interactions with their environment can change on subsecond scales. However, particle interactions can be hidden or invisible-even when measured with thermal noise sensitivity, leading to misconceptions about their binding behavior. Here, it is demonstrated how invisible particle interactions at the cell periphery become visible by MHz interferometric thermal noise tracking and frequency decomposition at a spectral update rate of only 0.5 s. The particle fluctuations are analyzed in radial and lateral directions by a viscoelastic modulus G(ω,tex ) over the experiment time tex , revealing a surprisingly similar, frequency dependent response for different cell types. This response behavior can be explained by a mathematical model for molecular scale elasticity and damping. The method to reveal hidden interactions is tested at two examples: the stiffening of macrophage filopodia tips within 2 s with particle contact invisible by the fluctuation width. Second, the extent and stiffness of the soft cell glycocalyx is measured, which can be sensed by a particle only on microsecond-timescales, but which remains invisible on time-average. This concept study shows how to uncover hidden cellular interactions, if particle motions are measured at high-speed.
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Affiliation(s)
- Felix Jünger
- Laboratory for Bio- and Nano-Photonics, Department of Microsystems Engineering (IMTEK), University of Freiburg, Georges-Koehler-Allee 102, 79110, Freiburg, Germany
| | - Alexander Rohrbach
- Laboratory for Bio- and Nano-Photonics, Department of Microsystems Engineering (IMTEK), University of Freiburg, Georges-Koehler-Allee 102, 79110, Freiburg, Germany
- CIBSS - Centre for Integrative Biological Signaling Studies, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
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2
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Liu P, Li Y, Ye Y, Chen J, Li R, Zhang Q, Li Y, Wang W, Meng Q, Ou J, Yang Z, Sun W, Gu W. The genome and antigen proteome analysis of Spiroplasma mirum. Front Microbiol 2022; 13:996938. [PMID: 36406404 PMCID: PMC9666726 DOI: 10.3389/fmicb.2022.996938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023] Open
Abstract
Spiroplasma mirum, small motile wall-less bacteria, was originally isolated from a rabbit tick and had the ability to infect newborn mice and caused cataracts. In this study, the whole genome and antigen proteins of S. mirum were comparative analyzed and investigated. Glycolysis, pentose phosphate pathway, arginine metabolism, nucleotide biosynthesis, and citrate fermentation were found in S. mirum, while trichloroacetic acid, fatty acids metabolism, phospholipid biosynthesis, terpenoid biosynthesis, lactose-specific PTS, and cofactors synthesis were completely absent. The Sec systems of S. mirum consist of SecA, SecE, SecDF, SecG, SecY, and YidC. Signal peptidase II was identified in S. mirum, but no signal peptidase I. The relative gene order in S. mirum is largely conserved. Genome analysis of available species in Mollicutes revealed that they shared only 84 proteins. S. mirum genome has 381 pseudogenes, accounting for 31.6% of total protein-coding genes. This is the evidence that spiroplasma genome is under an ongoing genome reduction. Immunoproteomics, a new scientific technique combining proteomics and immunological analytical methods, provided the direction of our research on S. mirum. We identified 49 proteins and 11 proteins (9 proteins in common) in S. mirum by anti-S. mirum serum and negative serum, respectively. Forty proteins in S. mirum were identified in relation to the virulence. All these proteins may play key roles in the pathogeny and can be used in the future for diagnoses and prevention.
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Affiliation(s)
- Peng Liu
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Basic Medical School, Hengyang Medical School, Institute of Pathogenic Biology, University of South China, Hengyang, China
| | - Yuxin Li
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Basic Medical School, Hengyang Medical School, Institute of Pathogenic Biology, University of South China, Hengyang, China
| | - Youyuan Ye
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Basic Medical School, Hengyang Medical School, Institute of Pathogenic Biology, University of South China, Hengyang, China
| | - Jiaxin Chen
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Basic Medical School, Hengyang Medical School, Institute of Pathogenic Biology, University of South China, Hengyang, China
| | - Rong Li
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Basic Medical School, Hengyang Medical School, Institute of Pathogenic Biology, University of South China, Hengyang, China
| | - Qinyi Zhang
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Basic Medical School, Hengyang Medical School, Institute of Pathogenic Biology, University of South China, Hengyang, China
| | - Yuan Li
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Basic Medical School, Hengyang Medical School, Institute of Pathogenic Biology, University of South China, Hengyang, China
| | - Wen Wang
- Key Laboratory for Aquatic Crustacean Diseases, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, China
| | - Qingguo Meng
- Key Laboratory for Aquatic Crustacean Diseases, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, China
| | - Jingyu Ou
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Basic Medical School, Hengyang Medical School, Institute of Pathogenic Biology, University of South China, Hengyang, China
| | - Zhujun Yang
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Basic Medical School, Hengyang Medical School, Institute of Pathogenic Biology, University of South China, Hengyang, China
| | - Wei Sun
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Wei Gu
- Key Laboratory for Aquatic Crustacean Diseases, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, China
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3
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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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4
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Meng Q, Liu P, Wang J, Wang Y, Hou L, Gu W, Wang W. Systematic analysis of the lysine acetylome of the pathogenic bacterium Spiroplasma eriocheiris reveals acetylated proteins related to metabolism and helical structure. J Proteomics 2016; 148:159-69. [PMID: 27498276 DOI: 10.1016/j.jprot.2016.08.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 07/28/2016] [Accepted: 08/02/2016] [Indexed: 10/21/2022]
Abstract
UNLABELLED Post-translational modifications such as acetylation are an essential regulatory mechanism of protein function. Spiroplasma eriocheiris, with no cell wall and a helical structure, is a novel pathogen of freshwater crustacean. There is no other evidence of acylation (such as succinylation and propionylation) except acetylation genes in S. eriocheiris concise genome. So the acetylation may play an important role in S. eriocheiris. Here, we conducted the first lysine acetylome in S. eriocheiris. We identified 2567 lysine acetylation sites in 555 proteins, which account for 44.69% of the total proteins in this bacterium. To date, this is the highest ratio of acetylated proteins that have been identified in bacteria. Fifteen types of acetylated peptide sequence motifs were revealed from the acetylome. Forty-five lysine-acetylated proteins showed homology with acetylated proteins previously identified from Escherichia coli, Vibrio parahemolyticus and Mycobacterium tuberculosis. Notably, most proteins in glycolysis and all proteins in the arginine deiminase system were acetylated. Meanwhile, the cell skeleton proteins (Fibril and Mrebs) were all acetylated the observed acetylation also played an important role in cell skeleton formation. The results imply previously unreported hidden layers of post-translational regulation in lysine acetylation that define the functional state of Spiroplasma. BIOLOGICAL SIGNIFICANCE This is the first time to analyze PTM of Spiroplasma. This is the highest ratio of acetylated proteins that have been identified in bacteria. S. eriocheiris lysine acetylome reveals acetylated proteins related to metabolism and helical structure. These data provide an important resource to elucidate the role of acetylation in Spiroplasma cellular physiology.
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Affiliation(s)
- Qingguo Meng
- Jiangsu Key Laboratory for Biodiversity & Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China; Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Peng Liu
- Jiangsu Key Laboratory for Biodiversity & Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China; Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Jian Wang
- Jiangsu Key Laboratory for Biodiversity & Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China; Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Yinghui Wang
- Jiangsu Key Laboratory for Biodiversity & Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China; Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Libo Hou
- Jiangsu Key Laboratory for Biodiversity & Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China; Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Wei Gu
- Jiangsu Key Laboratory for Biodiversity & Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China; Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Wen Wang
- Jiangsu Key Laboratory for Biodiversity & Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China; Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China.
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5
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Jünger F, Olshausen PV, Rohrbach A. Fast, label-free super-resolution live-cell imaging using rotating coherent scattering (ROCS) microscopy. Sci Rep 2016; 6:30393. [PMID: 27465033 PMCID: PMC4964612 DOI: 10.1038/srep30393] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 06/30/2016] [Indexed: 11/29/2022] Open
Abstract
Living cells are highly dynamic systems with cellular structures being often below the optical resolution limit. Super-resolution microscopes, usually based on fluorescence cell labelling, are usually too slow to resolve small, dynamic structures. We present a label-free microscopy technique, which can generate thousands of super-resolved, high contrast images at a frame rate of 100 Hertz and without any post-processing. The technique is based on oblique sample illumination with coherent light, an approach believed to be not applicable in life sciences because of too many interference artefacts. However, by circulating an incident laser beam by 360° during one image acquisition, relevant image information is amplified. By combining total internal reflection illumination with dark-field detection, structures as small as 150 nm become separable through local destructive interferences. The technique images local changes in refractive index through scattered laser light and is applied to living mouse macrophages and helical bacteria revealing unexpected dynamic processes.
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Affiliation(s)
- Felix Jünger
- Laboratory for Bio- and Nano-Photonics, Department of Microsystems Engineering, University of Freiburg, Germany
| | - Philipp V Olshausen
- Laboratory for Bio- and Nano-Photonics, Department of Microsystems Engineering, University of Freiburg, Germany.,Testo AG, Testo-Straße 1, 79853 Lenzkirch, Germany
| | - Alexander Rohrbach
- Laboratory for Bio- and Nano-Photonics, Department of Microsystems Engineering, University of Freiburg, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
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6
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Trachtenberg S, Schuck P, Phillips TM, Andrews SB, Leapman RD. A structural framework for a near-minimal form of life: mass and compositional analysis of the helical mollicute Spiroplasma melliferum BC3. PLoS One 2014; 9:e87921. [PMID: 24586297 PMCID: PMC3931623 DOI: 10.1371/journal.pone.0087921] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Accepted: 01/01/2014] [Indexed: 12/31/2022] Open
Abstract
Spiroplasma melliferum is a wall-less bacterium with dynamic helical geometry. This organism is geometrically well defined and internally well ordered, and has an exceedingly small genome. Individual cells are chemotactic, polar, and swim actively. Their dynamic helicity can be traced at the molecular level to a highly ordered linear motor (composed essentially of the proteins fib and MreB) that is positioned on a defined helical line along the internal face of the cell's membrane. Using an array of complementary, informationally overlapping approaches, we have taken advantage of this uniquely simple, near-minimal life-form and its helical geometry to analyze the copy numbers of Spiroplasma's essential parts, as well as to elucidate how these components are spatially organized to subserve the whole living cell. Scanning transmission electron microscopy (STEM) was used to measure the mass-per-length and mass-per-area of whole cells, membrane fractions, intact cytoskeletons and cytoskeletal components. These local data were fit into whole-cell geometric parameters determined by a variety of light microscopy modalities. Hydrodynamic data obtained by analytical ultracentrifugation allowed computation of the hydration state of whole living cells, for which the relative amounts of protein, lipid, carbohydrate, DNA, and RNA were also estimated analytically. Finally, ribosome and RNA content, genome size and gene expression were also estimated (using stereology, spectroscopy and 2D-gel analysis, respectively). Taken together, the results provide a general framework for a minimal inventory and arrangement of the major cellular components needed to support life.
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Affiliation(s)
- Shlomo Trachtenberg
- Dept of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
- * E-mail:
| | - Peter Schuck
- Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Terry M. Phillips
- Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, United States of America
| | - S. Brian Andrews
- Laboratory of Neurobiology, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Richard D. Leapman
- Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, United States of America
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7
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Lin L, Thanbichler M. Nucleotide-independent cytoskeletal scaffolds in bacteria. Cytoskeleton (Hoboken) 2013; 70:409-23. [PMID: 23852773 DOI: 10.1002/cm.21126] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 06/28/2013] [Accepted: 07/03/2013] [Indexed: 11/11/2022]
Abstract
Bacteria possess a diverse set of cytoskeletal proteins that mediate key cellular processes such as morphogenesis, cell division, DNA segregation, and motility. Similar to eukaryotic actin or tubulin, many of them require nucleotide binding and hydrolysis for proper polymerization and function. However, there is also a growing number of bacterial cytoskeletal elements that assemble in a nucleotide-independent manner, including intermediate filament-like structures as well several classes of bacteria-specific polymers. The members of this group form stable scaffolds that have architectural roles or act as localization factors recruiting other proteins to distinct positions within the cell. Here, we highlight the elements that constitute the nucleotide-independent cytoskeleton of bacteria and discuss their biological functions in different species.
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Affiliation(s)
- Lin Lin
- Max Planck Research Group "Prokaryotic Cell Biology", Max Planck Institute for Terrestrial Microbiology, Marburg, Germany; Faculty of Biology, Philipps-Universität, Marburg, Germany
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8
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Alexeev D, Kostrjukova E, Aliper A, Popenko A, Bazaleev N, Tyakht A, Selezneva O, Akopian T, Prichodko E, Kondratov I, Chukin M, Demina I, Galyamina M, Kamashev D, Vanyushkina A, Ladygina V, Levitskii S, Lazarev V, Govorun V. Application of Spiroplasma melliferum Proteogenomic Profiling for the Discovery of Virulence Factors and Pathogenicity Mechanisms in Host-associated Spiroplasmas. J Proteome Res 2011; 11:224-36. [DOI: 10.1021/pr2008626] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Dmitry Alexeev
- Russian Institute of Physico-Chemical Medicine, Malaya Pirogovskaya 1a,
Moscow, Russian Federation
- Moscow Institute of Physics and Technology - Bioinformatics Dolgoprudny,
Pervomayskaya 21 , Moscow 117303, Russian Federation
| | - Elena Kostrjukova
- Russian Institute of Physico-Chemical Medicine, Malaya Pirogovskaya 1a,
Moscow, Russian Federation
| | - Alexander Aliper
- Russian Institute of Physico-Chemical Medicine, Malaya Pirogovskaya 1a,
Moscow, Russian Federation
| | - Anna Popenko
- Russian Institute of Physico-Chemical Medicine, Malaya Pirogovskaya 1a,
Moscow, Russian Federation
| | - Nikolay Bazaleev
- Russian Institute of Physico-Chemical Medicine, Malaya Pirogovskaya 1a,
Moscow, Russian Federation
| | - Alexander Tyakht
- Russian Institute of Physico-Chemical Medicine, Malaya Pirogovskaya 1a,
Moscow, Russian Federation
| | - Oksana Selezneva
- Russian Institute of Physico-Chemical Medicine, Malaya Pirogovskaya 1a,
Moscow, Russian Federation
- Russian Research Centre Kurchatov Institute, pl. Akademika Kurchatova
1, Moscow 123182, Russian Federation
| | - Tatyana Akopian
- Russian Institute of Physico-Chemical Medicine, Malaya Pirogovskaya 1a,
Moscow, Russian Federation
| | - Elena Prichodko
- Russian Institute of Physico-Chemical Medicine, Malaya Pirogovskaya 1a,
Moscow, Russian Federation
| | - Ilya Kondratov
- Russian Institute of Physico-Chemical Medicine, Malaya Pirogovskaya 1a,
Moscow, Russian Federation
| | - Mikhail Chukin
- Russian Institute of Physico-Chemical Medicine, Malaya Pirogovskaya 1a,
Moscow, Russian Federation
| | - Irina Demina
- Russian Institute of Physico-Chemical Medicine, Malaya Pirogovskaya 1a,
Moscow, Russian Federation
| | - Maria Galyamina
- Russian Institute of Physico-Chemical Medicine, Malaya Pirogovskaya 1a,
Moscow, Russian Federation
| | - Dmitri Kamashev
- Russian Institute of Physico-Chemical Medicine, Malaya Pirogovskaya 1a,
Moscow, Russian Federation
- Russian Research Centre Kurchatov Institute, pl. Akademika Kurchatova
1, Moscow 123182, Russian Federation
| | - Anna Vanyushkina
- Russian Institute of Physico-Chemical Medicine, Malaya Pirogovskaya 1a,
Moscow, Russian Federation
- Russian Research Centre Kurchatov Institute, pl. Akademika Kurchatova
1, Moscow 123182, Russian Federation
| | - Valentina Ladygina
- Russian Institute of Physico-Chemical Medicine, Malaya Pirogovskaya 1a,
Moscow, Russian Federation
| | - Sergei Levitskii
- Russian Institute of Physico-Chemical Medicine, Malaya Pirogovskaya 1a,
Moscow, Russian Federation
- Russian Research Centre Kurchatov Institute, pl. Akademika Kurchatova
1, Moscow 123182, Russian Federation
| | - Vasily Lazarev
- Russian Institute of Physico-Chemical Medicine, Malaya Pirogovskaya 1a,
Moscow, Russian Federation
- Russian Research Centre Kurchatov Institute, pl. Akademika Kurchatova
1, Moscow 123182, Russian Federation
| | - Vadim Govorun
- Russian Institute of Physico-Chemical Medicine, Malaya Pirogovskaya 1a,
Moscow, Russian Federation
- Russian Research Centre Kurchatov Institute, pl. Akademika Kurchatova
1, Moscow 123182, Russian Federation
- M.M. Shemyakin–Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Ul. Miklukho-Maklaya,
16/10 , Moscow 117997, Russian Federation
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9
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Cohen-Krausz S, Cabahug PC, Trachtenberg S. The Monomeric, Tetrameric, and Fibrillar Organization of Fib: The Dynamic Building Block of the Bacterial Linear Motor of Spiroplasma melliferum BC3. J Mol Biol 2011; 410:194-213. [DOI: 10.1016/j.jmb.2011.04.067] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Revised: 04/18/2011] [Accepted: 04/27/2011] [Indexed: 10/18/2022]
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10
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Wada H, Netz RR. Hydrodynamics of helical-shaped bacterial motility. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009; 80:021921. [PMID: 19792165 DOI: 10.1103/physreve.80.021921] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2008] [Revised: 06/04/2009] [Indexed: 05/28/2023]
Abstract
To reveal the underlying hydrodynamic mechanism for the directed propulsion of the bacterium Spiroplasma, we formulate a coarse-grained elastic polymer model with domains of alternating helicities along the contour. Using hydrodynamic simulations and analytic arguments, we show that the propagation of helical domain walls leads to the directed propulsion of the cell body opposite to the domain-wall traveling direction. Several key features of Spiroplasma motility are reproduced by our model. We in particular show that the helical pitch angle observed for Spiroplasma meliferum, psi=35 degrees , is optimized for maximal swimming speed and energy-conversion efficiency. Our analytic theory based on the slender-body hydrodynamic approximation agrees very well with our numerical data demonstrating how the chirality switch propagating along the helical cell body is converted to a translational thrust for the cell body itself. We in detail consider thermal effects on the propulsion efficiency in the form of orientational fluctuations and conformational fluctuations of the helix shape. The body length dependence of the cell motility is studied numerically and compared to our approximate analytic theory. For fixed pitch angle psi=35 degrees , the swimming speed is maximized at a ratio of cell-body length to domain length of about 2-3, which are typical values for real cells. We also propose simple analytic arguments for an enhancement of the swimming velocity with increasing solution viscosity by taking into account the effects of transient confinement of a helical cell body in a polymeric meshwork. Comparison with a generalized theory for the swimming speed of flagellated bacteria in polymeric meshworks shows that the presence of a finite-sized bacterial head gives rise to a maximal swimming speed at a finite solution viscosity, whereas in the absence of a head the swimming speed monotonically increases with increasing viscosity.
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Affiliation(s)
- Hirofumi Wada
- Yukawa Institute for Theoretical Physics, Kyoto University, 606-8502 Kyoto, Japan
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11
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Abstract
Prokaryotic cells move through liquids or over moist surfaces by swimming, swarming, gliding, twitching or floating. An impressive diversity of motility mechanisms has evolved in prokaryotes. Movement can involve surface appendages, such as flagella that spin, pili that pull and Mycoplasma 'legs' that walk. Internal structures, such as the cytoskeleton and gas vesicles, are involved in some types of motility, whereas the mechanisms of some other types of movement remain mysterious. Regardless of the type of motility machinery that is employed, most motile microorganisms use complex sensory systems to control their movements in response to stimuli, which allows them to migrate to optimal environments.
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12
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Trachtenberg S, Dorward LM, Speransky VV, Jaffe H, Andrews SB, Leapman RD. Structure of the cytoskeleton of Spiroplasma melliferum BC3 and its interactions with the cell membrane. J Mol Biol 2008; 378:778-89. [PMID: 18400234 DOI: 10.1016/j.jmb.2008.02.020] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2007] [Revised: 02/04/2008] [Accepted: 02/12/2008] [Indexed: 10/22/2022]
Abstract
Spiroplasma melliferum is a wall-less bacterium with dynamic helical symmetry. Taking advantage of the simplicity of this primitive lifeform, we have used structural (electron tomography and freeze fracture of whole cells; cryoelectron tomography and diffraction analysis of isolated cytoskeletons) and proteomic approaches to elucidate the basic organizing principles of its minimal yet functional cytoskeleton. From among approximately 30 Spiroplasma proteins present in a highly purified cytoskeletal fraction, we identify three major putative structural proteins: Fib, MreB, and elongation factor Tu. Fib assembles into a single flattened ribbon that follows the shortest helical line just under the plasma membrane and acts as a linear motor, whereas MreB is present as a matching array of membrane-associated fibrils parallel and associated with the motor. We also identify a prominent previously unknown filamentous network that occupies much of the cytoplasm and appears to cross-link the ribosomes. The abundant potentially filament-forming protein elongation factor Tu may be a component of this network, but the tomography data are most consistent with DNA as the core component. The results provide new information on the minimal organization necessary to support the scaffolding and motile functions of a minimal cytoskeleton.
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Affiliation(s)
- Shlomo Trachtenberg
- Department of Membrane and Ultrastructure Research, The Hebrew University-Hadassah Medical School, PO Box 12272, Jerusalem 91120, Israel.
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13
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Wada H, Netz RR. Model for self-propulsive helical filaments: kink-pair propagation. PHYSICAL REVIEW LETTERS 2007; 99:108102. [PMID: 17930410 DOI: 10.1103/physrevlett.99.108102] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2007] [Indexed: 05/25/2023]
Abstract
Spiroplasma bacteria propel through viscous fluids by sending kinks or domain walls between regions of opposite handedness down their helical body. A simple elastic model for the domain-wall propagation is formulated and studied using hydrodynamic simulations and scaling arguments, giving good agreement with recent video-microscopy observations. It is shown that the observed helical bacterial pitch angle psi approximately 35 degrees is optimized for maximal speed and efficiency.
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Affiliation(s)
- Hirofumi Wada
- Physics Department, Technical University Munich, 85748 Garching, Germany
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14
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Abstract
Within a short period of time after the discovery of bacterial cytoskletons, major progress had been made in areas such as general spatial layout of cytoskeletons, their involvement in a variety of cellfunctions (shape control, cell division, chromosome segregation, cell motility). This progress was achieved by application of advanced investigation techniques. Homologs of eukaryotic actin, tubulin, and intermediate filaments were found in bacteria; cytoskeletal proteins not closely or not at all related to any of these major cytoskeletal proteins were discovered in a number of bacteria such as Mycoplasmas, Spiroplasmas, Spirochetes, Treponema, Caulobacter. A structural role for bacterial elongation factor Tu was indicated. On the basis of this new thinking, new approaches in biotechnology and new drugs are on the way.
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