1
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Fazeli A, Thakore V, Ala-Nissila T, Karttunen M. Non-Stokesian dynamics of magnetic helical nanoswimmers under confinement. PNAS NEXUS 2024; 3:pgae182. [PMID: 38765716 PMCID: PMC11102084 DOI: 10.1093/pnasnexus/pgae182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/19/2024] [Indexed: 05/22/2024]
Abstract
Electromagnetically propelled helical nanoswimmers offer great potential for nanorobotic applications. Here, the effect of confinement on their propulsion is characterized using lattice-Boltzmann simulations. Two principal mechanisms give rise to their forward motion under confinement: (i) pure swimming and (ii) the thrust created by the differential pressure due to confinement. Under strong confinement, they face greater rotational drag but display a faster propulsion for fixed driving frequency in agreement with experimental findings. This is due to the increased differential pressure created by the boundary walls when they are sufficiently close to each other and the particle. We have proposed two analytical relations (i) for predicting the swimming speed of an unconfined particle as a function of its angular speed and geometrical properties, and (ii) an empirical expression to accurately predict the propulsion speed of a confined swimmer as a function of the degree of confinement and its unconfined swimming speed. At low driving frequencies and degrees of confinement, the systems retain the expected linear behavior consistent with the predictions of the Stokes equation. However, as the driving frequency and/or the degree of confinement increase, their impact on propulsion leads to increasing deviations from the Stokesian regime and emergence of nonlinear behavior.
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Affiliation(s)
- Alireza Fazeli
- Department of Mathematics, Western University, London, ON N6A 5B7, Canada
- Center for Advanced Materials and Biomaterials Research, Western University, London, ON N6A 5B7, Canada
| | - Vaibhav Thakore
- Department of Mathematics, Western University, London, ON N6A 5B7, Canada
- Center for Advanced Materials and Biomaterials Research, Western University, London, ON N6A 5B7, Canada
| | - Tapio Ala-Nissila
- Multiscale Statistical and Quantum Physics Group, Quantum Technology Finland Centre of Excellence, Department of Applied Physics, Aalto University, FI-00076 Aalto, Espoo, Finland
- Interdisciplinary Centre for Mathematical Modelling, Department of Mathematical Sciences, Loughborough University, Loughborough, Leicestershire LE11 3TU, UK
| | - Mikko Karttunen
- Department of Physics and Astronomy, Western University, London, ON N6A 5B7, Canada
- Department of Chemistry, Western University, London, ON N6A 3K7, Canada
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2
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Takahashi D, Miyata M, Fujiwara I. Assembly properties of Spiroplasma MreB involved in swimming motility. J Biol Chem 2023:104793. [PMID: 37150324 DOI: 10.1016/j.jbc.2023.104793] [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: 01/26/2023] [Revised: 04/29/2023] [Accepted: 05/02/2023] [Indexed: 05/09/2023] Open
Abstract
Bacterial actin MreB forms filaments formed of antiparallel double strand units. The wall-less helical bacterium Spiroplasma has five MreB homologs (MreB1-5), some of which are involved in an intra-cellular ribbon for driving the bacterium's swimming motility. Although the interaction between MreB units is important for understanding Spiroplasma swimming, the interaction modes of each ribbon component are unclear. Here, we examined the assembly properties of Spiroplasma eriocheiris MreB5 (SpeMreB5), one of the ribbon component proteins that forms sheets. Electron microscopy (EM) revealed that sheet formation was inhibited under acidic conditions and bundle structures were formed under acidic and neutral conditions with low ionic strength. We also used solution assays and identified four properties of SpeMreB5 bundles as follows: (I) bundle formation followed sheet formation; (II) electrostatic interactions were required for bundle formation; (III) the positively charged and unstructured C-terminal region contributed to promoting lateral interactions for bundle formation; and (IV) bundle formation required Mg2+ at neutral pH but was inhibited by divalent cations under acidic pH conditions. During these studies, we also characterized two aggregation modes of SpeMreB5 with distinct responses to ATP. These properties will shed light on SpeMreB5 assembly dynamics at the molecular level.
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Affiliation(s)
- Daichi Takahashi
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan
| | - Makoto Miyata
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan; The OMU Advanced Research Center for Natural Science and Technology, Osaka Metropolitan University, Osaka, Japan
| | - Ikuko Fujiwara
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan; The OMU Advanced Research Center for Natural Science and Technology, Osaka Metropolitan University, Osaka, Japan; Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan.
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3
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Swimming Motility Assays of Spiroplasma. Methods Mol Biol 2023; 2646:373-381. [PMID: 36842131 DOI: 10.1007/978-1-0716-3060-0_31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
Spiroplasma swim in liquids without the use of the bacterial flagella. This small helical bacterium propels itself by generating kinks that travel down the cell body. The kink translation is unidirectional, from the leading pole to the lagging pole, during cell swimming in viscous environments. This protocol describes a swimming motility assay of Spiroplasma eriocheiris for visualizing kink translations of the absolute handedness of the body helix with optical microscopy.
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4
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Takahashi D, Miyata M. Sequence analyses of a lipoprotein conserved with bacterial actins responsible for swimming motility of wall-less helical Spiroplasma. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000713. [PMID: 37033705 PMCID: PMC10074174 DOI: 10.17912/micropub.biology.000713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/07/2023] [Accepted: 03/09/2023] [Indexed: 04/11/2023]
Abstract
Spiroplasma is a genus of pathogenic or commensal cell-wall-deficient helical bacterium. Spiroplasma -specific protein fibril and five classes of bacterial actins, MreB1-5, are involved in a helical ribbon structure responsible for helical-cell morphology and swimming motility. A gene for a hypothetical protein-SPE_1229, 7th protein-has been found in the locus coding mreB s. In this study, we characterized the 7th protein using in silico methods and found that it could be a lipoprotein whose gene is encoded downstream of mreB3 and conserved in a clade of Spiroplasma .
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Affiliation(s)
- Daichi Takahashi
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan
| | - Makoto Miyata
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan
- The OMU Advanced Research Center for Natural Science and Technology, Osaka Metropolitan University, Osaka, Japan
- Correspondence to: Makoto Miyata (
)
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5
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Kiyama H, Kakizawa S, Sasajima Y, Tahara YO, Miyata M. Reconstitution of a minimal motility system based on Spiroplasma swimming by two bacterial actins in a synthetic minimal bacterium. SCIENCE ADVANCES 2022; 8:eabo7490. [PMID: 36449609 PMCID: PMC9710875 DOI: 10.1126/sciadv.abo7490] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 10/14/2022] [Indexed: 05/24/2023]
Abstract
Motility is one of the most important features of life, but its evolutionary origin remains unknown. In this study, we focused on Spiroplasma, commensal, or parasitic bacteria. They swim by switching the helicity of a ribbon-like cytoskeleton that comprises six proteins, each of which evolved from a nucleosidase and bacterial actin called MreB. We expressed these proteins in a synthetic, nonmotile minimal bacterium, JCVI-syn3B, whose reduced genome was computer-designed and chemically synthesized. The synthetic bacterium exhibited swimming motility with features characteristic of Spiroplasma swimming. Moreover, combinations of Spiroplasma MreB4-MreB5 and MreB1-MreB5 produced a helical cell shape and swimming. These results suggest that the swimming originated from the differentiation and coupling of bacterial actins, and we obtained a minimal system for motility of the synthetic bacterium.
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Affiliation(s)
- Hana Kiyama
- Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
- Graduate School of Science, Osaka Metropolitan University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Shigeyuki Kakizawa
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Yuya Sasajima
- Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
- Graduate School of Science, Osaka Metropolitan University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Yuhei O. Tahara
- Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
- Graduate School of Science, Osaka Metropolitan University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Makoto Miyata
- Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
- Graduate School of Science, Osaka Metropolitan University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
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6
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Takahashi D, Fujiwara I, Sasajima Y, Narita A, Imada K, Miyata M. ATP-dependent polymerization dynamics of bacterial actin proteins involved in Spiroplasma swimming. Open Biol 2022; 12:220083. [PMID: 36285441 PMCID: PMC9597168 DOI: 10.1098/rsob.220083] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
MreB is a bacterial protein belonging to the actin superfamily. This protein polymerizes into an antiparallel double-stranded filament that determines cell shape by maintaining cell wall synthesis. Spiroplasma eriocheiris, a helical wall-less bacterium, has five MreB homologous (SpeMreB1-5) that probably contribute to swimming motility. Here, we investigated the structure, ATPase activity and polymerization dynamics of SpeMreB3 and SpeMreB5. SpeMreB3 polymerized into a double-stranded filament with possible antiparallel polarity, while SpeMreB5 formed sheets which contained the antiparallel filament, upon nucleotide binding. SpeMreB3 showed slow Pi release owing to the lack of an amino acid motif conserved in the catalytic centre of MreB family proteins. Our SpeMreB3 crystal structures and analyses of SpeMreB3 and SpeMreB5 variants showed that the amino acid motif probably plays a role in eliminating a nucleophilic water proton during ATP hydrolysis. Sedimentation assays suggest that SpeMreB3 has a lower polymerization activity than SpeMreB5, though their polymerization dynamics are qualitatively similar to those of other actin superfamily proteins, in which pre-ATP hydrolysis and post-Pi release states are unfavourable for them to remain as filaments.
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Affiliation(s)
- Daichi Takahashi
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan,Graduate School of Science, Osaka City University, Osaka, Japan
| | - Ikuko Fujiwara
- Graduate School of Science, Osaka City University, Osaka, Japan,The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka, Japan,Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Yuya Sasajima
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan,Graduate School of Science, Osaka City University, Osaka, Japan
| | - Akihiro Narita
- Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Katsumi Imada
- Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Makoto Miyata
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan,The OMU Advanced Research Center for Natural Science and Technology, Osaka Metropolitan University, Osaka, Japan,Graduate School of Science, Osaka City University, Osaka, Japan,The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka, Japan
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7
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Godar S, Oristian J, Hinsch V, Wentworth K, Lopez E, Amlashi P, Enverso G, Markley S, Alper JD. Light chain 2 is a Tctex-type related axonemal dynein light chain that regulates directional ciliary motility in Trypanosoma brucei. PLoS Pathog 2022; 18:e1009984. [PMID: 36155669 PMCID: PMC9536576 DOI: 10.1371/journal.ppat.1009984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/06/2022] [Accepted: 08/26/2022] [Indexed: 01/04/2023] Open
Abstract
Flagellar motility is essential for the cell morphology, viability, and virulence of pathogenic kinetoplastids. Trypanosoma brucei flagella beat with a bending wave that propagates from the flagellum's tip to its base, rather than base-to-tip as in other eukaryotes. Thousands of dynein motor proteins coordinate their activity to drive ciliary bending wave propagation. Dynein-associated light and intermediate chains regulate the biophysical mechanisms of axonemal dynein. Tctex-type outer arm dynein light chain 2 (LC2) regulates flagellar bending wave propagation direction, amplitude, and frequency in Chlamydomonas reinhardtii. However, the role of Tctex-type light chains in regulating T. brucei motility is unknown. Here, we used a combination of bioinformatics, in-situ molecular tagging, and immunofluorescence microscopy to identify a Tctex-type light chain in the procyclic form of T. brucei (TbLC2). We knocked down TbLC2 expression using RNAi in both wild-type and FLAM3, a flagellar attachment zone protein, knockdown cells and quantified TbLC2's effects on trypanosome cell biology and biophysics. We found that TbLC2 knockdown reduced the directional persistence of trypanosome cell swimming, induced an asymmetric ciliary bending waveform, modulated the bias between the base-to-tip and tip-to-base beating modes, and increased the beating frequency. Together, our findings are consistent with a model of TbLC2 as a down-regulator of axonemal dynein activity that stabilizes the forward tip-to-base beating ciliary waveform characteristic of trypanosome cells. Our work sheds light on axonemal dynein regulation mechanisms that contribute to pathogenic kinetoplastids' unique tip-to-base ciliary beating nature and how those mechanisms underlie dynein-driven ciliary motility more generally.
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Affiliation(s)
- Subash Godar
- Department of Physics and Astronomy, College of Science, Clemson University, Clemson, South Carolina, United States of America
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, United States of America
| | - James Oristian
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, United States of America
- Department of Genetics and Biochemistry, College of Science, Clemson University, Clemson, South Carolina, United States of America
| | - Valerie Hinsch
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, United States of America
- Department of Genetics and Biochemistry, College of Science, Clemson University, Clemson, South Carolina, United States of America
| | - Katherine Wentworth
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, United States of America
- Department of Biological Sciences, College of Science, Clemson University, Clemson, South Carolina, United States of America
| | - Ethan Lopez
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, United States of America
- Department of Genetics and Biochemistry, College of Science, Clemson University, Clemson, South Carolina, United States of America
| | - Parastoo Amlashi
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, United States of America
- Department of Biological Sciences, College of Science, Clemson University, Clemson, South Carolina, United States of America
| | - Gerald Enverso
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, United States of America
- Department of Biological Sciences, College of Science, Clemson University, Clemson, South Carolina, United States of America
| | - Samantha Markley
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, United States of America
- Department of Biological Sciences, College of Science, Clemson University, Clemson, South Carolina, United States of America
| | - Joshua Daniel Alper
- Department of Physics and Astronomy, College of Science, Clemson University, Clemson, South Carolina, United States of America
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, United States of America
- Department of Biological Sciences, College of Science, Clemson University, Clemson, South Carolina, United States of America
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8
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Sasajima Y, Miyata M. Prospects for the Mechanism of Spiroplasma Swimming. Front Microbiol 2021; 12:706426. [PMID: 34512583 PMCID: PMC8432965 DOI: 10.3389/fmicb.2021.706426] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/12/2021] [Indexed: 11/18/2022] Open
Abstract
Spiroplasma are helical bacteria that lack a peptidoglycan layer. They are widespread globally as parasites of arthropods and plants. Their infectious processes and survival are most likely supported by their unique swimming system, which is unrelated to well-known bacterial motility systems such as flagella and pili. Spiroplasma swims by switching the left- and right-handed helical cell body alternately from the cell front. The kinks generated by the helicity shift travel down along the cell axis and rotate the cell body posterior to the kink position like a screw, pushing the water backward and propelling the cell body forward. An internal structure called the "ribbon" has been focused to elucidate the mechanisms for the cell helicity formation and swimming. The ribbon is composed of Spiroplasma-specific fibril protein and a bacterial actin, MreB. Here, we propose a model for helicity-switching swimming focusing on the ribbon, in which MreBs generate a force like a bimetallic strip based on ATP energy and switch the handedness of helical fibril filaments. Cooperative changes of these filaments cause helicity to shift down the cell axis. Interestingly, unlike other motility systems, the fibril protein and Spiroplasma MreBs can be traced back to their ancestors. The fibril protein has evolved from methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidase, which is essential for growth, and MreBs, which function as a scaffold for peptidoglycan synthesis in walled bacteria.
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Affiliation(s)
- Yuya Sasajima
- Department of Biology, Graduate School of Science, Osaka City University, Osaka, Japan
| | - Makoto Miyata
- Department of Biology, Graduate School of Science, Osaka City University, Osaka, Japan
- The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka, Japan
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9
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Takahashi D, Fujiwara I, Miyata M. Phylogenetic origin and sequence features of MreB from the wall-less swimming bacteria Spiroplasma. Biochem Biophys Res Commun 2020; 533:638-644. [PMID: 33066960 DOI: 10.1016/j.bbrc.2020.09.060] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 01/01/2023]
Abstract
Spiroplasma are wall-less bacteria which belong to the phylum Tenericutes that evolved from Firmicutes including Bacillus subtilis. Spiroplasma swim by a mechanism unrelated to widespread bacterial motilities, such as flagellar motility, and caused by helicity switching with kinks traveling along the helical cell body. The swimming force is likely generated by five classes of bacterial actin homolog MreBs (SMreBs 1-5) involved in the helical bone structure. We analyzed sequences of SMreBs to clarify their phylogeny and sequence features. The maximum likelihood method based on around 5000 MreB sequences showed that the phylogenetic tree was divided into several radiations. SMreBs formed a clade adjacent to the radiation of MreBH, an MreB isoform of Firmicutes. Sequence comparisons of SMreBs and Bacillus MreBs were also performed to clarify the features of SMreB. Catalytic glutamic acid and threonine were substituted to aspartic acid and lysine, respectively, in SMreB3. In SMreBs 2 and 4, amino acids involved in inter- and intra-protofilament interactions were significantly different from those in Bacillus MreBs. A membrane-binding region was not identified in most SMreBs 1 and 4 unlike many walled-bacterial MreBs. SMreB5 had a significantly longer C-terminal region than the other MreBs, which possibly forms protein-protein interactions. These features may support the functions responsible for the unique mechanism of Spiroplasma swimming.
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Affiliation(s)
- Daichi Takahashi
- Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka, 558-8585, Japan
| | - Ikuko Fujiwara
- Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka, 558-8585, Japan; The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Sumiyoshi-ku, Osaka, 558-8585, Japan
| | - Makoto Miyata
- Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka, 558-8585, Japan; The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Sumiyoshi-ku, Osaka, 558-8585, Japan.
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10
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Miyata M, Robinson RC, Uyeda TQP, Fukumori Y, Fukushima SI, Haruta S, Homma M, Inaba K, Ito M, Kaito C, Kato K, Kenri T, Kinosita Y, Kojima S, Minamino T, Mori H, Nakamura S, Nakane D, Nakayama K, Nishiyama M, Shibata S, Shimabukuro K, Tamakoshi M, Taoka A, Tashiro Y, Tulum I, Wada H, Wakabayashi KI. Tree of motility - A proposed history of motility systems in the tree of life. Genes Cells 2020; 25:6-21. [PMID: 31957229 PMCID: PMC7004002 DOI: 10.1111/gtc.12737] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/11/2019] [Accepted: 11/17/2019] [Indexed: 12/27/2022]
Abstract
Motility often plays a decisive role in the survival of species. Five systems of motility have been studied in depth: those propelled by bacterial flagella, eukaryotic actin polymerization and the eukaryotic motor proteins myosin, kinesin and dynein. However, many organisms exhibit surprisingly diverse motilities, and advances in genomics, molecular biology and imaging have showed that those motilities have inherently independent mechanisms. This makes defining the breadth of motility nontrivial, because novel motilities may be driven by unknown mechanisms. Here, we classify the known motilities based on the unique classes of movement‐producing protein architectures. Based on this criterion, the current total of independent motility systems stands at 18 types. In this perspective, we discuss these modes of motility relative to the latest phylogenetic Tree of Life and propose a history of motility. During the ~4 billion years since the emergence of life, motility arose in Bacteria with flagella and pili, and in Archaea with archaella. Newer modes of motility became possible in Eukarya with changes to the cell envelope. Presence or absence of a peptidoglycan layer, the acquisition of robust membrane dynamics, the enlargement of cells and environmental opportunities likely provided the context for the (co)evolution of novel types of motility.
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Affiliation(s)
- Makoto Miyata
- Department of Biology, Graduate School of Science, Osaka City University, Osaka, Japan.,The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka, Japan
| | - Robert C Robinson
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, Japan.,School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Taro Q P Uyeda
- Department of Physics, Faculty of Science and Technology, Waseda University, Tokyo, Japan
| | - Yoshihiro Fukumori
- Faculty of Natural System, Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan.,WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Shun-Ichi Fukushima
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
| | - Shin Haruta
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
| | - Michio Homma
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Kazuo Inaba
- Shimoda Marine Research Center, University of Tsukuba, Shizuoka, Japan
| | - Masahiro Ito
- Graduate School of Life Sciences, Toyo University, Gunma, Japan
| | - Chikara Kaito
- Laboratory of Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Kentaro Kato
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, Miyagi, Japan
| | - Tsuyoshi Kenri
- Laboratory of Mycoplasmas and Haemophilus, Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Seiji Kojima
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Hiroyuki Mori
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Shuichi Nakamura
- Department of Applied Physics, Graduate School of Engineering, Tohoku University, Miyagi, Japan
| | - Daisuke Nakane
- Department of Physics, Gakushuin University, Tokyo, Japan
| | - Koji Nakayama
- Department of Microbiology and Oral Infection, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Masayoshi Nishiyama
- Department of Physics, Faculty of Science and Engineering, Kindai University, Osaka, Japan
| | - Satoshi Shibata
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Katsuya Shimabukuro
- Department of Chemical and Biological Engineering, National Institute of Technology, Ube College, Yamaguchi, Japan
| | - Masatada Tamakoshi
- Department of Molecular Biology, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Azuma Taoka
- Faculty of Natural System, Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan.,WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Yosuke Tashiro
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Isil Tulum
- Department of Botany, Faculty of Science, Istanbul University, Istanbul, Turkey
| | - Hirofumi Wada
- Department of Physics, Graduate School of Science and Engineering, Ritsumeikan University, Shiga, Japan
| | - Ken-Ichi Wakabayashi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Kanagawa, Japan
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11
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Chae MK, Kim Y, Johner A, Lee NK. Adsorption of a Helical Filament Subject to Thermal Fluctuations. Polymers (Basel) 2020; 12:polym12010192. [PMID: 31936860 PMCID: PMC7023455 DOI: 10.3390/polym12010192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/02/2020] [Accepted: 01/05/2020] [Indexed: 02/06/2023] Open
Abstract
We consider semiflexible chains governed by preferred curvature and twist and their flexural and twist moduli. These filaments possess a helical rather than straight three-dimensional (3D) ground state and we call them helical filaments (H-filament). Depending on the moduli, the helical shape may be smeared by thermal fluctuations. Secondary superhelical structures are expected to form on top of the specific local structure of biofilaments, as is documented for vimentin. We study confinement and adsorption of helical filaments utilizing both a combination of numerical simulations and analytical theory. We investigate overall chain shapes, transverse chain fluctuations, loop and tail distributions, and energy distributions along the chain together with the mean square average height of the monomers 〈 z 2 〉 . The number fraction of adsorbed monomers serves as an order parameter for adsorption. Signatures of adsorbed helical polymers are the occurrence of 3D helical loops/tails and spiral or wavy quasi-flat shapes. None of these arise for the Worm-Like-Chain, whose straight ground state can be embedded in a plane.
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Affiliation(s)
- M.-K. Chae
- Department of Physics and Astronomy, Sejong University, Seoul 05006, Korea
| | - Y. Kim
- Department of Physics and Astronomy, Sejong University, Seoul 05006, Korea
| | - A. Johner
- Institute Charles Sadron, CNRS 23 Rue du Loess, 67034 Strasbourg CEDEX 2, France
- Correspondence: or (A.J.); (N.-K.L.)
| | - N.-K. Lee
- Department of Physics and Astronomy, Sejong University, Seoul 05006, Korea
- Institute Charles Sadron, CNRS 23 Rue du Loess, 67034 Strasbourg CEDEX 2, France
- Correspondence: or (A.J.); (N.-K.L.)
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12
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Boudet JF, Mathelié-Guinlet M, Vilquin A, Douliez JP, Béven L, Kellay H. Large variability in the motility of spiroplasmas in media of different viscosities. Sci Rep 2018; 8:17138. [PMID: 30459324 PMCID: PMC6244147 DOI: 10.1038/s41598-018-35326-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 10/27/2018] [Indexed: 11/09/2022] Open
Abstract
Spiroplasmas are bacteria that do not possess flagella and their motility is linked to kink propagation coupled to changes in the cell body helicity. While the motility of bacteria with flagellar motion has been studied extensively, less work has been devoted to the motility of spiroplasmas. We first show that the motility of such bacteria has large variability from individual to individual as well as large fluctuations in time. The Brownian motion of such bacteria both in orientation and translation is also highlighted. We propose a simple model to disentangle the different components of this motility by examining trajectories of single bacteria in different viscosity solvents. The mean velocity of the bacteria turns out to depend on the viscosity of the medium as it increases with viscosity. Further, the temporal fluctuations of the bacteria motility turn out to be very strong with a direct link to tumbling events particular to this bacteria.
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Affiliation(s)
- J F Boudet
- U. Bordeaux, Laboratoire Ondes et Matière d'Aquitaine, UMR 5798 CNRS/U. Bordeaux, 33405, Talence, France
| | - M Mathelié-Guinlet
- U. Bordeaux, Laboratoire Ondes et Matière d'Aquitaine, UMR 5798 CNRS/U. Bordeaux, 33405, Talence, France
| | - A Vilquin
- U. Bordeaux, Laboratoire Ondes et Matière d'Aquitaine, UMR 5798 CNRS/U. Bordeaux, 33405, Talence, France
| | - J P Douliez
- UMR 1332, Biologie du Fruit et Pathologie, Univ. Bordeaux, INRA, 33882, Villenave d'Ornon, France
| | - L Béven
- UMR 1332, Biologie du Fruit et Pathologie, Univ. Bordeaux, INRA, 33882, Villenave d'Ornon, France
| | - H Kellay
- U. Bordeaux, Laboratoire Ondes et Matière d'Aquitaine, UMR 5798 CNRS/U. Bordeaux, 33405, Talence, France.
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13
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Chae MK, Kim Y, Johner A, Lee NK. Super-helical filaments at surfaces: dynamics and elastic responses. SOFT MATTER 2018; 14:2346-2356. [PMID: 29498722 DOI: 10.1039/c7sm01990d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Bio-filaments often behave in a way unexpected from the standard semi-flexible polymer chain model (WLC), when squeezed to a surface, confined in microfluidic channels or clamped by their end. This calls for the super-helical filament model, going beyond WLC, where the filament forms a helix much wider than its diameter. We study this model using Brownian dynamics simulations, focusing on filaments confined to a surface by a strong potential. We analyze shapes and shape fluctuations under tension where excited states comprising a number of inflection points (twist-kink) can be stabilized. Pulling/releasing experiments during a cycle of increasing/decreasing tension show hysteresis. We find that the excited state, once established, is long-lived and the life time grows with the filament length cubed. Twist-kink diffusion involves position (filament shape) dependent friction for which we provide analytical expression. Dynamic responses to tension are investigated via numerical simulations and several mechanisms of shape relaxation are found and rationalized.
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Affiliation(s)
- Min-Kyung Chae
- Department of Physics, Sejong University, Seoul 05006, South Korea.
| | - Yunha Kim
- Department of Physics, Sejong University, Seoul 05006, South Korea.
| | - Albert Johner
- Institute Charles Sadron, CNRS 23 Rue du Loess, 67034 Strasbourg cedex 2, France
| | - Nam-Kyung Lee
- Department of Physics, Sejong University, Seoul 05006, South Korea.
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14
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Geometric somersaults of helical chains through twist propagation. ARTIFICIAL LIFE AND ROBOTICS 2018. [DOI: 10.1007/s10015-017-0388-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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15
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Terahara N, Tulum I, Miyata M. Transformation of crustacean pathogenic bacterium Spiroplasma eriocheiris and expression of yellow fluorescent protein. Biochem Biophys Res Commun 2017; 487:488-493. [PMID: 28363870 DOI: 10.1016/j.bbrc.2017.03.144] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 03/26/2017] [Indexed: 10/19/2022]
Abstract
Spiroplasma eriocheiris, the cause of crab trembling disease, is a wall-less bacterium, related to Mycoplasmas, measuring 2.0-10.0 μm long. It features a helical cell shape and a unique swimming mechanism that does not use flagella; instead, it moves by switching the cell helicity at a kink traveling from the front to the tail. S. eriocheiris seems to use a novel chemotactic system that is based on the frequency of reversal swimming behaviors rather than the conventional two-component system, which is generally essential for bacterial chemotaxis. To identify the genes involved in these novel mechanisms, we developed a transformation system by using oriC plasmid harboring the tetracycline resistant gene, tetM, which is under the control of a strong promoter for an abundant protein, elongation factor-Tu. The transformation efficiency achieved was 1.6 × 10-5 colony forming unit (CFU) for 1 μg DNA, enabling the expression of the enhanced yellow fluorescent protein (EYFP).
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Affiliation(s)
- Natsuho Terahara
- Department of Biology, Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan.
| | - Isil Tulum
- Department of Biology, Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan; The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan.
| | - Makoto Miyata
- Department of Biology, Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan; The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan.
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16
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Alcanzare MMT, Thakore V, Ollila STT, Karttunen M, Ala-Nissila T. Controlled propulsion and separation of helical particles at the nanoscale. SOFT MATTER 2017; 13:2148-2154. [PMID: 28225092 DOI: 10.1039/c6sm02437h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Controlling the motion of nano and microscale objects in a fluid environment is a key factor in designing optimized tiny machines that perform mechanical tasks such as transport of drugs or genetic material in cells, fluid mixing to accelerate chemical reactions, and cargo transport in microfluidic chips. Directed motion is made possible by the coupled translational and rotational motion of asymmetric particles. A current challenge in achieving directed and controlled motion at the nanoscale lies in overcoming random Brownian motion due to thermal fluctuations in the fluid. We use a hybrid lattice-Boltzmann molecular dynamics method with full hydrodynamic interactions and thermal fluctuations to demonstrate that controlled propulsion of individual nanohelices in an aqueous environment is possible. We optimize the propulsion velocity and the efficiency of externally driven nanohelices. We quantify the importance of the thermal effects on the directed motion by calculating the Péclet number for various shapes, number of turns and pitch lengths of the helices. Consistent with the experimental microscale separation of chiral objects, our results indicate that in the presence of thermal fluctuations at Péclet numbers >10, chiral particles follow the direction of propagation according to its handedness and the direction of the applied torque making separation of chiral particles possible at the nanoscale. Our results provide criteria for the design and control of helical machines at the nanoscale.
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Affiliation(s)
- Maria Michiko T Alcanzare
- COMP CoE at the Department of Applied Physics, Aalto University School of Science, P.O. Box 11000, FIN-00076 Aalto, Espoo, Finland.
| | - Vaibhav Thakore
- COMP CoE at the Department of Applied Physics, Aalto University School of Science, P.O. Box 11000, FIN-00076 Aalto, Espoo, Finland.
| | - Santtu T T Ollila
- Varian Medical Systems Finland, Paciuksenkatu 21, 00270 Helsinki, Finland
| | - Mikko Karttunen
- Department of Mathematics and Computer Science & Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, MetaForum 5600 MB, The Netherlands and Department of Chemistry & Applied Mathematics, Western University, 1151 Richmond Street, London, Ontario, Canada N6A 5B7
| | - Tapio Ala-Nissila
- COMP CoE at the Department of Applied Physics, Aalto University School of Science, P.O. Box 11000, FIN-00076 Aalto, Espoo, Finland. and Department of Physics, Brown University, Box 1843, 182 Hope Street Barus & Holley, Providence, Rhode Island 02912-1843, USA and Department of Mathematical Science and Department of Physics, Loughborough University, Loughborough, LE11 3TU, UK
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17
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Yanao T, Hino T. Geometric somersaults of a polymer chain through cyclic twisting motions. Phys Rev E 2017; 95:012409. [PMID: 28208442 DOI: 10.1103/physreve.95.012409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Indexed: 11/07/2022]
Abstract
This study explores the significance of geometric angle shifts, which we call geometric somersaults, arising from cyclic twisting motions of a polymer chain. A five-bead polymer chain serves as a concise and minimal model of a molecular shaft throughout this study. We first show that this polymer chain can change its orientation about its longitudinal axis largely, e.g., 120^{∘}, under conditions of zero total angular momentum by changing the two dihedral angles in a cyclic manner. This phenomenon is an example of the so-called "falling cat" phenomenon, where a falling cat undergoes a geometric somersault by changing its body shape under conditions of zero total angular momentum. We then extend the geometric somersault of the polymer chain to a noisy and viscous environment, where the polymer chain is steered by external driving forces. This extension shows that the polymer chain can achieve an orientation change keeping its total angular momentum and total external torque fluctuating around zero in a noisy and viscous environment. As an application, we argue that the geometric somersault of the polymer chain by 120^{∘} may serve as a prototypical and coarse-grained model for the rotary motion of the central shaft of ATP synthase (F_{O}F_{1}-ATPase). This geometric somersault is in clear contrast to the standard picture for the rotary motion of the central shaft as a rigid body, which generally incurs nonzero total angular momentum and nonzero total external torque. The power profile of the geometric somersault implies a preliminary mechanism for elastic power transmission. The results of this study may be of fundamental interest in twisting and rotary motions of biomolecules.
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Affiliation(s)
- Tomohiro Yanao
- Department of Applied Mechanics and Aerospace Engineering, Waseda University, Tokyo 169-8555, Japan
| | - Taiko Hino
- Department of Applied Mechanics and Aerospace Engineering, Waseda University, Tokyo 169-8555, Japan
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18
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Liu P, Zheng H, Meng Q, Terahara N, Gu W, Wang S, Zhao G, Nakane D, Wang W, Miyata M. Chemotaxis without Conventional Two-Component System, Based on Cell Polarity and Aerobic Conditions in Helicity-Switching Swimming of Spiroplasma eriocheiris. Front Microbiol 2017; 8:58. [PMID: 28217108 PMCID: PMC5289999 DOI: 10.3389/fmicb.2017.00058] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 01/09/2017] [Indexed: 11/13/2022] Open
Abstract
Spiroplasma eriocheiris is a pathogen that causes mass mortality in Chinese mitten crab, Eriocheir sinensis. S. eriocheiris causes tremor disease and infects almost all of the artificial breeding crustaceans, resulting in disastrous effects on the aquaculture economy in China. S. eriocheiris is a wall-less helical bacterium, measuring 2.0 to 10.0 μm long, and can swim up to 5 μm per second in a viscous medium without flagella by switching the cell helicity at a kink traveling from the front to the tail. In this study, we showed that S. eriocheiris performs chemotaxis without the conventional two-component system, a system commonly found in bacterial chemotaxis. The chemotaxis of S. eriocheiris was observed more clearly when the cells were cultivated under anaerobic conditions. The cells were polarized as evidenced by a tip structure, swimming in the direction of the tip, and were shown to reverse their swimming direction in response to attractants. Triton X-100 treatment revealed the internal structure, a dumbbell-shaped core in the tip that is connected by a flat ribbon, which traces the shortest line in the helical cell shape from the tip to the other pole. Sixteen proteins were identified as the components of the internal structure by mass spectrometry, including Fibril protein and four types of MreB proteins.
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Affiliation(s)
- Peng Liu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal UniversityJiangsu, China; Department of Biology, Graduate School of Science, Osaka City UniversityOsaka, Japan
| | - Huajun Zheng
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai Shanghai, China
| | - Qingguo Meng
- Jiangsu Key Laboratory for Biodiversity and Biotechnology and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University Jiangsu, China
| | - Natsuho Terahara
- Department of Biology, Graduate School of Science, Osaka City University Osaka, Japan
| | - Wei Gu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University Jiangsu, China
| | - Shengyue Wang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai Shanghai, China
| | - Guoping Zhao
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai Shanghai, China
| | - Daisuke Nakane
- Department of Physics, Gakushuin University Tokyo, Japan
| | - Wen Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University Jiangsu, China
| | - Makoto Miyata
- Department of Biology, Graduate School of Science, Osaka City UniversityOsaka, Japan; The OCU Advanced Research Institute for Natural Science and Technology, Osaka City UniversityOsaka, Japan
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19
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Wada H. Structural mechanics and helical geometry of thin elastic composites. SOFT MATTER 2016; 12:7386-7397. [PMID: 27510457 DOI: 10.1039/c6sm01090c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Helices are ubiquitous in nature, and helical shape transition is often observed in residually stressed bodies, such as composites, wherein materials with different mechanical properties are glued firmly together to form a whole body. Inspired by a variety of biological examples, the basic physical mechanism responsible for the emergence of twisting and bending in such thin composite structures has been extensively studied. Here, we propose a simplified analytical model wherein a slender membrane tube undergoes a helical transition driven by the contraction of an elastic ribbon bound to the membrane surface. We analytically predict the curvature and twist of an emergent helix as functions of differential strains and elastic moduli, which are confirmed by our numerical simulations. Our results may help understand shapes observed in different biological systems, such as spiral bacteria, and could be applied to novel designs of soft machines and robots.
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Affiliation(s)
- Hirofumi Wada
- Department of Physics, Ritsumeikan University, Kusatsu, 525-8577 Shiga, Japan.
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20
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Miyata M, Hamaguchi T. Integrated Information and Prospects for Gliding Mechanism of the Pathogenic Bacterium Mycoplasma pneumoniae. Front Microbiol 2016; 7:960. [PMID: 27446003 PMCID: PMC4923136 DOI: 10.3389/fmicb.2016.00960] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Accepted: 06/02/2016] [Indexed: 01/21/2023] Open
Abstract
Mycoplasma pneumoniae forms a membrane protrusion at a cell pole and is known to adhere to solid surfaces, including animal cells, and can glide on these surfaces with a speed up to 1 μm per second. Notably, gliding appears to be involved in the infectious process in addition to providing the bacteria with a means of escaping the host's immune systems. However, the genome of M. pneumoniae does not encode any of the known genes found in other bacterial motility systems or any conventional motor proteins that are responsible for eukaryotic motility. Thus, further analysis of the mechanism underlying M. pneumoniae gliding is warranted. The gliding machinery formed as the membrane protrusion can be divided into the surface and internal structures. On the surface, P1 adhesin, a 170 kDa transmembrane protein forms an adhesin complex with other two proteins. The internal structure features a terminal button, paired plates, and a bowl (wheel) complex. In total, the organelle is composed of more than 15 proteins. By integrating the currently available information by genetics, microscopy, and structural analyses, we have suggested a working model for the architecture of the organelle. Furthermore, in this article, we suggest and discuss a possible mechanism of gliding based on the structural model, in which the force generated around the bowl complex transmits through the paired plates, reaching the adhesin complex, resulting in the repeated catch of sialylated oligosaccharides on the host surface by the adhesin complex.
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Affiliation(s)
- Makoto Miyata
- Department of Biology, Graduate School of Science, Osaka City UniversityOsaka, Japan; The OCU Advanced Research Institute for Natural Science and Technology, Osaka City UniversityOsaka, Japan
| | - Tasuku Hamaguchi
- Department of Biology, Graduate School of Science, Osaka City UniversityOsaka, Japan; The OCU Advanced Research Institute for Natural Science and Technology, Osaka City UniversityOsaka, Japan
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21
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Reprint of “Prospects for the gliding mechanism of Mycoplasma mobile”. Curr Opin Microbiol 2015; 28:122-8. [PMID: 26711226 DOI: 10.1016/j.mib.2015.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Mycoplasma mobile forms gliding machinery at a cell pole and glides continuously in the direction of the cell pole at up to 4.5 μm per second on solid surfaces such as animal cells. This motility system is not related to those of any other bacteria or eukaryotes. M. mobile uses ATP energy to repeatedly catch, pull, and release sialylated oligosaccharides on host cells with its approximately 50-nm long legs. The gliding machinery is a large structure composed of huge surface proteins and internal jellyfish-like structure. This system may have developed from an accidental combination between an adhesin and a rotary ATPase, both of which are essential for the adhesive parasitic life of Mycoplasmas.
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22
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Miyata M, Hamaguchi T. Prospects for the gliding mechanism of Mycoplasma mobile. Curr Opin Microbiol 2015; 29:15-21. [PMID: 26500189 DOI: 10.1016/j.mib.2015.08.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 08/01/2015] [Accepted: 08/03/2015] [Indexed: 01/06/2023]
Abstract
Mycoplasma mobile forms gliding machinery at a cell pole and glides continuously in the direction of the cell pole at up to 4.5μm per second on solid surfaces such as animal cells. This motility system is not related to those of any other bacteria or eukaryotes. M. mobile uses ATP energy to repeatedly catch, pull, and release sialylated oligosaccharides on host cells with its approximately 50-nm long legs. The gliding machinery is a large structure composed of huge surface proteins and internal jellyfish-like structure. This system may have developed from an accidental combination between an adhesin and a rotary ATPase, both of which are essential for the adhesive parasitic life of Mycoplasmas.
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Affiliation(s)
- Makoto Miyata
- Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka, Japan.
| | - Tasuku Hamaguchi
- Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka, Japan
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23
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Pham JT, Morozov A, Crosby AJ, Lindner A, du Roure O. Deformation and shape of flexible, microscale helices in viscous flow. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:011004. [PMID: 26274116 DOI: 10.1103/physreve.92.011004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Indexed: 06/04/2023]
Abstract
We examine experimentally the deformation of flexible, microscale helical ribbons with nanoscale thickness subject to viscous flow in a microfluidic channel. Two aspects of flexible microhelices are quantified: the overall shape of the helix and the viscous frictional properties. The frictional coefficients determined by our experiments are consistent with calculated values in the context of resistive-force theory. The deformation of helices by viscous flow is well described by nonlinear finite extensibility. Under distributed loading, the pitch distribution is nonuniform, and from this we identify both linear and nonlinear behavior along the contour length of a single helix. Moreover, flexible helices are found to display reversible global to local helical transitions at a high flow rate.
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Affiliation(s)
- Jonathan T Pham
- Polymer Science and Engineering Department, University of Massachusetts Amherst, 120 Governors Drive, Amherst, Massachusetts 01003, USA
- PMMH-ESPCI-ParisTech, UMR 7636 CNRS-ESPCI, Université Pierre et Marie Curie, Université Paris Diderot, 10 rue Vauquelin, 75005 Paris, France
| | - Alexander Morozov
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Alfred J Crosby
- Polymer Science and Engineering Department, University of Massachusetts Amherst, 120 Governors Drive, Amherst, Massachusetts 01003, USA
| | - Anke Lindner
- PMMH-ESPCI-ParisTech, UMR 7636 CNRS-ESPCI, Université Pierre et Marie Curie, Université Paris Diderot, 10 rue Vauquelin, 75005 Paris, France
| | - Olivia du Roure
- PMMH-ESPCI-ParisTech, UMR 7636 CNRS-ESPCI, Université Pierre et Marie Curie, Université Paris Diderot, 10 rue Vauquelin, 75005 Paris, France
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24
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Hirashima T. Pattern Formation of an Epithelial Tubule by Mechanical Instability during Epididymal Development. Cell Rep 2014; 9:866-73. [DOI: 10.1016/j.celrep.2014.09.041] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 08/22/2014] [Accepted: 09/22/2014] [Indexed: 10/24/2022] Open
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25
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Tarama M, Menzel AM, ten Hagen B, Wittkowski R, Ohta T, Löwen H. Dynamics of a deformable active particle under shear flow. J Chem Phys 2013; 139:104906. [DOI: 10.1063/1.4820416] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Mitsusuke Tarama
- Department of Physics, Kyoto University, Kyoto 606-8502, Japan
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, D-40225 Düsseldorf, Germany
- Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
- Department of Physics, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Andreas M. Menzel
- Department of Physics, Kyoto University, Kyoto 606-8502, Japan
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, D-40225 Düsseldorf, Germany
| | - Borge ten Hagen
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, D-40225 Düsseldorf, Germany
| | - Raphael Wittkowski
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3JZ, United Kingdom
| | - Takao Ohta
- Department of Physics, Kyoto University, Kyoto 606-8502, Japan
- Department of Physics, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
- Soft Matter Center, Ochanomizu University, Tokyo 112-0012, Japan
| | - Hartmut Löwen
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, D-40225 Düsseldorf, Germany
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26
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Tarama M, Ohta T. Oscillatory motions of an active deformable particle. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 87:062912. [PMID: 23848753 DOI: 10.1103/physreve.87.062912] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Indexed: 06/02/2023]
Abstract
We investigate dynamics of an active particle in which shape deformations occur spontaneously. In two dimensions, the deformations are expanded in terms of the Fourier series and the couplings of different modes are taken into consideration truncated up to lower orders. We focus our attention on the special symmetrical structure between the coupled equations of n- and 2n-mode deformations for n=1, and those for n=2. We show that an oscillatory bifurcation occurs for n=2, which corresponds mathematically to the bifurcation for n=1 where a straight motion becomes unstable and a circular motion appears. At the oscillatory state, the particle undergoes either a spinning motion or a standing oscillation of shape deformations.
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27
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Tarama M, Ohta T. Spinning motion of a deformable self-propelled particle in two dimensions. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2012; 24:464129. [PMID: 23114593 DOI: 10.1088/0953-8984/24/46/464129] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We investigate the dynamics of a single deformable self-propelled particle which undergoes a spinning motion in a two-dimensional space. Equations of motion are derived from symmetry arguments for three kinds of variable. One is a vector which represents the velocity of the center of mass. The second is a traceless symmetric tensor representing deformation. The third is an antisymmetric tensor for spinning degree of freedom. By numerical simulations, we have obtained a variety of dynamical states due to interplay between the spinning motion and the deformation. The bifurcations of these dynamical states are analyzed by the simplified equations of motion.
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Wada H. Geometry of twist transport in a rotating elastic rod. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 84:042901. [PMID: 22181209 DOI: 10.1103/physreve.84.042901] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Indexed: 05/31/2023]
Abstract
An elastic rod rotating in a viscous fluid undergoes a shape transition from a twirling (axial spinning) to a whirling state (crankshafting motion) at a certain critical frequency [Wolgemuth et al., Phys. Rev. Lett. 84, 1623 (2000)]. The physical properties of such whirling rods are largely unknown, owing to their strongly nonlinear character. We analytically and numerically demonstrate that this dynamical transition occurs to reduce the viscous energy dissipation. A simple geometric interpretation underlying this observation is also given. These results provide a fundamental scenario for viscous twist transport in flexible filaments and are potentially important in the analysis of biopolymer dynamics such as DNA supercoiling during transcriptions.
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Affiliation(s)
- Hirofumi Wada
- Yukawa Institute for Theoretical Physics, Kyoto University, Sakyo, 606-8502 Kyoto, Japan
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Uppaluri S, Nagler J, Stellamanns E, Heddergott N, Herminghaus S, Engstler M, Pfohl T. Impact of microscopic motility on the swimming behavior of parasites: straighter trypanosomes are more directional. PLoS Comput Biol 2011; 7:e1002058. [PMID: 21698122 PMCID: PMC3116898 DOI: 10.1371/journal.pcbi.1002058] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Accepted: 03/31/2011] [Indexed: 11/18/2022] Open
Abstract
Microorganisms, particularly parasites, have developed sophisticated swimming mechanisms to cope with a varied range of environments. African Trypanosomes, causative agents of fatal illness in humans and animals, use an insect vector (the Tsetse fly) to infect mammals, involving many developmental changes in which cell motility is of prime importance. Our studies reveal that differences in cell body shape are correlated with a diverse range of cell behaviors contributing to the directional motion of the cell. Straighter cells swim more directionally while cells that exhibit little net displacement appear to be more bent. Initiation of cell division, beginning with the emergence of a second flagellum at the base, correlates to directional persistence. Cell trajectory and rapid body fluctuation correlation analysis uncovers two characteristic relaxation times: a short relaxation time due to strong body distortions in the range of 20 to 80 ms and a longer time associated with the persistence in average swimming direction in the order of 15 seconds. Different motility modes, possibly resulting from varying body stiffness, could be of consequence for host invasion during distinct infective stages.
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Affiliation(s)
- Sravanti Uppaluri
- Max-Planck-Institute for Dynamics and Self-Organization, Göttingen, Germany
| | - Jan Nagler
- Max-Planck-Institute for Dynamics and Self-Organization, Göttingen, Germany
- Institute for Nonlinear Dynamics, Faculty of Physics, Georg-August-Universität, Göttingen, Germany
| | - Eric Stellamanns
- Max-Planck-Institute for Dynamics and Self-Organization, Göttingen, Germany
| | - Niko Heddergott
- Biozentrum, Department for Cell and Developmental Biology, University of Würzburg, Würzburg, Germany
| | | | - Markus Engstler
- Biozentrum, Department for Cell and Developmental Biology, University of Würzburg, Würzburg, Germany
| | - Thomas Pfohl
- Max-Planck-Institute for Dynamics and Self-Organization, Göttingen, Germany
- Department of Chemistry, University of Basel, Basel, Switzerland
- * E-mail:
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