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Biomolecules
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Recent Advances in Supramolecular Motility Machinery of Microorganisms
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Recent Advances in Supramolecular Motility Machinery of Microorganisms

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Molecular Biophysics: Structure, Dynamics, and Function".

Deadline for manuscript submissions: closed (31 December 2024) | Viewed by 9950

Special Issue Editors

Dr. Tohru Minamino

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Guest Editor
Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
Interests: bacterial flagella; bacterial motility; bacterial protein secretion; macromolecular assembly; energy transduction
Special Issues, Collections and Topics in MDPI journals
Dr. Yusuke V. Morimoto

E-Mail Website
Guest Editor
Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka, Japan
Interests: cell motility; signal transduction; cellular slime mold; bacterial flagella; intracellular pH; fluorescence microscopy
Dr. Daisuke Nakane

E-Mail
Guest Editor
Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, Tokyo, Japan
Interests: bacterial motility; gliding motility; type IV pili; optical microscopy

Special Issue Information

Dear Colleagues,

Microorganisms use their own motility machinery to move in a variety of environments, and their locomotion is regulated by complex sensory signal transduction pathways that allow microorganisms to migrate towards more favorable environments and away from less favorable environments for survival. The motility apparatus is a supramolecular protein complex containing motor proteins that convert electrochemical or chemical energy to mechanical works for locomotion. Furthermore, the motor proteins can autonomously adjust their mechanical functions in response to changes in the environment. As a result, the motor machines have adapted to function in environments of the habitat of microorganisms.

Because locomotion is one of the most fascinating aspects of live organisms, supramolecular motility machines continue to fascinate many researchers. To date, 18 different types of motility systems have been identified on our planet. This Special Issue on Biomolecules is dedicated to covering recent understanding and perspectives of supramolecular motility machinery derived from bacteria, archaea, and other microorganisms. Our aim is to compile articles describing recent advances in the structure, assembly, and function of various motor protein complexes including bacterial flagella, type IV pili, archaella, and adhesion-based gliding machinery.

Dr. Tohru Minamino
Dr. Yusuke V. Morimoto
Dr. Daisuke Nakane
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biomolecules is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • motor proteins
  • motility
  • taxis
  • force generation
  • signal transduction

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Published Papers (11 papers)

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Research

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16 pages, 4826 KiB  
Article
Assembly Formation of P65 Protein, Featured by an Intrinsically Disordered Region Involved in Gliding Machinery of Mycoplasma pneumoniae
by Masaru Yabe, Takuma Toyonaga, Miki Kinoshita, Yukio Furukawa, Tasuku Hamaguchi, Yuhei O. Tahara, Munehito Arai, Katsumi Imada and Makoto Miyata
Biomolecules 2025, 15(3), 429; https://doi.org/10.3390/biom15030429 - 17 Mar 2025
Viewed by 466
Abstract
Mycoplasma pneumoniae is a human pathogen that glides on host cell surfaces by a repeated catch and release mechanism using sialylated oligosaccharides. At a pole, this organism forms a protrusion called an attachment organelle composed of surface structures, including an adhesin complex and [...] Read more.
Mycoplasma pneumoniae is a human pathogen that glides on host cell surfaces by a repeated catch and release mechanism using sialylated oligosaccharides. At a pole, this organism forms a protrusion called an attachment organelle composed of surface structures, including an adhesin complex and an internal core structure. To clarify the structure and function of the attachment organelle, we focused on a core component, P65, which is essential for stabilization of the adjacent surface and core proteins P30 and HMW2, respectively. Analysis of its amino acid sequence (405 residues) suggested that P65 contains an intrinsically disordered region (residues 1–217) and coiled-coil regions (residues 226–247, 255–283, and 286–320). Four protein fragments and the full-length P65 were analyzed by size exclusion chromatography, analytical centrifugation, circular dichroism spectroscopy, small-angle X-ray scattering, limited proteolysis, and negative staining electron microscopy. The results showed that P65 formed a multimer composed of a central globule with 30 and 23 nm axes and four to six projections 14 nm in length. Our data suggest that the C-terminal region of P65 is responsible for multimerization, while the intrinsically disordered N-terminal region forms a filament. These assignments and roles of P65 in the attachment organelle are discussed. Full article
(This article belongs to the Special Issue Recent Advances in Supramolecular Motility Machinery of Microorganisms)
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13 pages, 2902 KiB  
Article
Sodium-Dependent Conformational Change in Flagellar Stator Protein MotS from Bacillus subtilis
by Norihiro Takekawa, Ayaka Yamaguchi, Koki Nishiuchi, Maria Uehori, Miki Kinoshita, Tohru Minamino and Katsumi Imada
Biomolecules 2025, 15(2), 302; https://doi.org/10.3390/biom15020302 - 18 Feb 2025
Viewed by 554
Abstract
The bacterial flagellar motor consists of a rotor and stator units and is driven by ion flow through the stator. The activation of the ion flow is coupled with the anchoring of the stator units to the peptidoglycan layer by the stator B-subunit [...] Read more.
The bacterial flagellar motor consists of a rotor and stator units and is driven by ion flow through the stator. The activation of the ion flow is coupled with the anchoring of the stator units to the peptidoglycan layer by the stator B-subunit around the rotor. Gram-negative bacteria, such as Salmonella and Vibrio, change the conformation of the N-terminal helix of the periplasmic domain of the B-subunit to anchor the stator units. However, a recent high-speed atomic force microscopic study has suggested that the periplasmic domain of MotS, the stator B-subunit of the sodium (Na+)-driven stator of Bacillus subtilis, a gram-positive bacterium, unfolds at low external Na+ concentrations and folds at high Na+ concentrations to anchor the stator units. Here, we report the crystal structures of MotS68–242, a periplasmic fragment of MotS, from B. subtilis at high and low Na+ concentrations. We also performed far-UV CD spectroscopic analysis of the wild-type MotS68–242 and MotS78–242 proteins and mutant variants of MotS68–242 under high and low Na+ concentrations and found that the N-terminal disordered region of MotS68–242 shows a Na+-dependent coil–helix transition. We propose a mechanism of the Na+-dependent structural transition of Bs-MotS to anchor the stator units. Full article
(This article belongs to the Special Issue Recent Advances in Supramolecular Motility Machinery of Microorganisms)
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15 pages, 5468 KiB  
Article
Regulatory Role of a Hydrophobic Core in the FliG C-Terminal Domain in the Rotary Direction of a Flagellar Motor
by Tatsuro Nishikino, Akihiro Hatano, Seiji Kojima and Michio Homma
Biomolecules 2025, 15(2), 212; https://doi.org/10.3390/biom15020212 - 1 Feb 2025
Viewed by 666
Abstract
A flagellar motor can rotate either counterclockwise (CCW) or clockwise (CW), and rotational switching is triggered by conformational changes in FliG, although the molecular mechanism is still unknown. Here, we found that cheY deletion, which locks motor rotation in the CCW direction, restored [...] Read more.
A flagellar motor can rotate either counterclockwise (CCW) or clockwise (CW), and rotational switching is triggered by conformational changes in FliG, although the molecular mechanism is still unknown. Here, we found that cheY deletion, which locks motor rotation in the CCW direction, restored the motility abolished by the fliG L259Q mutation. We found that the CCW-biased fliG G214S mutation also restored the swimming of the L259Q mutant, but the CW-biased fliG G215A mutation did not. Since the L259 residue participates in forming the FliG hydrophobic core at its C-terminal domain, mutations were introduced into residues structurally closer to L259, and their motility was examined. Two mutants, D251R and L329Q, exhibited CW-biased rotation. Our results suggest that mutations in the hydrophobic core of FliGC collapse its conformational switching and/or stator interaction; however, the CCW state of the rotor enables rotation even with this disruption. Full article
(This article belongs to the Special Issue Recent Advances in Supramolecular Motility Machinery of Microorganisms)
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Review

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12 pages, 974 KiB  
Review
How Does the Archaellum Work?
by Morgan Beeby and Bertram Daum
Biomolecules 2025, 15(4), 465; https://doi.org/10.3390/biom15040465 - 21 Mar 2025
Viewed by 320
Abstract
The archaellum is the simplest known molecular propeller. An analogue of bacterial flagella, archaella are long helical tails found in Archaea that are rotated by cell-envelope-embedded rotary motors to exert thrust for cell motility. Despite their simplicity, however, they are less well studied, [...] Read more.
The archaellum is the simplest known molecular propeller. An analogue of bacterial flagella, archaella are long helical tails found in Archaea that are rotated by cell-envelope-embedded rotary motors to exert thrust for cell motility. Despite their simplicity, however, they are less well studied, and how they work remains only partially understood. Here we describe four key aspects of their function: assembly, the transition from assembly to rotation, the mechanics of rotation, and how rotation generates thrust. We outline future research directions that will enhance our understanding of archaellar function. Full article
(This article belongs to the Special Issue Recent Advances in Supramolecular Motility Machinery of Microorganisms)
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12 pages, 1487 KiB  
Review
Type IV Pili in Thermophilic Bacteria: Mechanisms and Ecological Implications
by Naoki A. Uemura and Daisuke Nakane
Biomolecules 2025, 15(4), 459; https://doi.org/10.3390/biom15040459 - 21 Mar 2025
Viewed by 499
Abstract
Type IV pili (T4P) machinery is critical for bacterial surface motility, protein secretion, and DNA uptake. This review highlights the ecological significance of T4P-dependent motility in Thermus thermophilus, a thermophilic bacterium isolated from hot springs. Unlike swimming motility, the T4P machinery enables [...] Read more.
Type IV pili (T4P) machinery is critical for bacterial surface motility, protein secretion, and DNA uptake. This review highlights the ecological significance of T4P-dependent motility in Thermus thermophilus, a thermophilic bacterium isolated from hot springs. Unlike swimming motility, the T4P machinery enables bacteria to move over two-dimensional surfaces through repeated cycles of extension and retraction of pilus filaments. Notably, T. thermophilus exhibits upstream-directed migration under shear stress, known as rheotaxis, which appears to represent an adaptive strategy unique to thermophilic bacteria thriving in rapid water flows. Furthermore, T4P contributes to the capture of DNA and phages, indicating their multifunctionality in natural environments. Understanding the T4P dynamics provides insights into bacterial survival and evolution in extreme habitats. Full article
(This article belongs to the Special Issue Recent Advances in Supramolecular Motility Machinery of Microorganisms)
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17 pages, 3256 KiB  
Review
Chemotaxis and Related Signaling Systems in Vibrio cholerae
by Fuga Omori, Hirotaka Tajima, Sotaro Asaoka, So-ichiro Nishiyama, Yoshiyuki Sowa and Ikuro Kawagishi
Biomolecules 2025, 15(3), 434; https://doi.org/10.3390/biom15030434 - 18 Mar 2025
Viewed by 598
Abstract
The motility and chemotaxis of Vibrio cholerae, the bacterial pathogen responsible for cholera, play crucial roles in both environmental survival and infection. Understanding their molecular mechanisms is therefore essential not only for fundamental biology but also for infection control and therapeutic development. [...] Read more.
The motility and chemotaxis of Vibrio cholerae, the bacterial pathogen responsible for cholera, play crucial roles in both environmental survival and infection. Understanding their molecular mechanisms is therefore essential not only for fundamental biology but also for infection control and therapeutic development. The bacterium’s sheathed, polar flagellum—its motility organelle—is powered by a sodium-driven motor. This motor’s rotation is regulated by the chemotaxis (Che) signaling system, with a histidine kinase, CheA, and a response regulator, CheY, serving as the central processing unit. However, V. cholerae possesses two additional, parallel Che signaling systems whose physiological functions remain unclear. Furthermore, the bacterium harbors over 40 receptors/transducers that interact with CheA homologs, forming a complex regulatory network likely adapted to diverse environmental cues. Despite significant progress, many aspects of these systems remain to be elucidated. Here, we summarize the current understanding to facilitate future research. Full article
(This article belongs to the Special Issue Recent Advances in Supramolecular Motility Machinery of Microorganisms)
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12 pages, 1998 KiB  
Review
Scrutinizing Stator Rotation in the Bacterial Flagellum: Reconciling Experiments and Switching Models
by Ayush Joshi and Pushkar P. Lele
Biomolecules 2025, 15(3), 355; https://doi.org/10.3390/biom15030355 - 1 Mar 2025
Viewed by 756
Abstract
The bacterial flagellar motor is one of the few known rotary motors, powering motility and chemotaxis. The mechanisms underlying its rotation and the switching of its rotational direction are fundamental problems in biology that are of significant interest. Recent high-resolution studies of the [...] Read more.
The bacterial flagellar motor is one of the few known rotary motors, powering motility and chemotaxis. The mechanisms underlying its rotation and the switching of its rotational direction are fundamental problems in biology that are of significant interest. Recent high-resolution studies of the flagellar motor have transformed our understanding of the motor, revealing a novel gear mechanism where a membranous pentamer of MotA proteins rotates around a cell wall-anchored dimer of MotB proteins to turn the contacting flagellar rotor. A derivative model suggests that significant changes in rotor diameter occur during switching, enabling each MotA5MotB2 stator unit to shift between internal and external gear configurations, causing clockwise (CW) and counterclockwise (CCW) motor rotation, respectively. However, recent structural work favors a mechanism where the stator units dynamically swing back and forth between the two gear configurations without significant changes in rotor diameter. Given the intricate link between the switching model and the gear mechanism for flagellar rotation, a critical evaluation of the underlying assumptions is crucial for refining switching models. This review scrutinizes key assumptions within prevailing models of flagellar rotation and switching, identifies knowledge gaps, and proposes avenues for future biophysical tests. Full article
(This article belongs to the Special Issue Recent Advances in Supramolecular Motility Machinery of Microorganisms)
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35 pages, 3056 KiB  
Review
Multiple Mechanisms to Regulate Actin Functions: “Fundamental” Versus Lineage-Specific Mechanisms and Hierarchical Relationships
by Taro Q. P. Uyeda, Yosuke Yamazaki, Saku T. Kijima, Taro Q. P. Noguchi and Kien Xuan Ngo
Biomolecules 2025, 15(2), 279; https://doi.org/10.3390/biom15020279 - 13 Feb 2025
Viewed by 787
Abstract
Eukaryotic actin filaments play a central role in numerous cellular functions, with each function relying on the interaction of actin filaments with specific actin-binding proteins. Understanding the mechanisms that regulate these interactions is key to uncovering how actin filaments perform diverse roles at [...] Read more.
Eukaryotic actin filaments play a central role in numerous cellular functions, with each function relying on the interaction of actin filaments with specific actin-binding proteins. Understanding the mechanisms that regulate these interactions is key to uncovering how actin filaments perform diverse roles at different cellular locations. Several distinct classes of actin regulatory mechanisms have been proposed and experimentally supported. However, these mechanisms vary in their nature and hierarchy. For instance, some operate under the control of others, highlighting hierarchical relationships. Additionally, while certain mechanisms are fundamental and ubiquitous across eukaryotes, others are lineage-specific. Here, we emphasize the fundamental importance and functional significance of the following actin regulatory mechanisms: the biochemical regulation of actin nucleators, the ATP hydrolysis-dependent aging of actin filaments, thermal fluctuation- and mechanical strain-dependent conformational changes of actin filaments, and cooperative conformational changes induced by actin-binding proteins. Full article
(This article belongs to the Special Issue Recent Advances in Supramolecular Motility Machinery of Microorganisms)
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20 pages, 1872 KiB  
Review
Nano-Scale Video Imaging of Motility Machinery by High-Speed Atomic Force Microscopy
by Steven John McArthur, Kenichi Umeda and Noriyuki Kodera
Biomolecules 2025, 15(2), 257; https://doi.org/10.3390/biom15020257 - 10 Feb 2025
Viewed by 899
Abstract
Motility is a vital aspect of many forms of life, with a wide range of highly conserved as well as highly unique systems adapted to the needs of various organisms and environments. While many motility systems are well studied using structural techniques like [...] Read more.
Motility is a vital aspect of many forms of life, with a wide range of highly conserved as well as highly unique systems adapted to the needs of various organisms and environments. While many motility systems are well studied using structural techniques like X-ray crystallography and electron microscopy, as well as fluorescence microscopy methodologies, it is difficult to directly determine the relationship between the shape and movement of a motility system due to a notable gap in spatiotemporal resolution. Bridging this gap as well as understanding the dynamic molecular movements that underpin motility mechanisms has been challenging. The advent of high-speed atomic force microscopy (HS-AFM) has provided a new window into understanding these nano-scale machines and the dynamic processes underlying motility. In this review, we highlight some of the advances in this field, ranging from reconstituted systems and purified higher-order supramolecular complexes to live cells, in both prokaryotic and eukaryotic contexts. Full article
(This article belongs to the Special Issue Recent Advances in Supramolecular Motility Machinery of Microorganisms)
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17 pages, 3426 KiB  
Review
Decoding Bacterial Motility: From Swimming States to Patterns and Chemotactic Strategies
by Xiang-Yu Zhuang and Chien-Jung Lo
Biomolecules 2025, 15(2), 170; https://doi.org/10.3390/biom15020170 - 23 Jan 2025
Viewed by 1250
Abstract
The bacterial flagellum serves as a crucial propulsion apparatus for motility and chemotaxis. Bacteria employ complex swimming patterns to perform essential biological tasks. These patterns involve transitions between distinct swimming states, driven by flagellar motor rotation, filament polymorphism, and variations in flagellar arrangement [...] Read more.
The bacterial flagellum serves as a crucial propulsion apparatus for motility and chemotaxis. Bacteria employ complex swimming patterns to perform essential biological tasks. These patterns involve transitions between distinct swimming states, driven by flagellar motor rotation, filament polymorphism, and variations in flagellar arrangement and configuration. Over the past two decades, advancements in fluorescence staining technology applied to bacterial flagella have led to the discovery of diverse bacterial movement states and intricate swimming patterns. This review provides a comprehensive overview of nano-filament observation methodologies, swimming states, swimming patterns, and the physical mechanisms underlying chemotaxis. These novel insights and ongoing research have the potential to inspire the design of innovative active devices tailored for operation in low-Reynolds-number environments. Full article
(This article belongs to the Special Issue Recent Advances in Supramolecular Motility Machinery of Microorganisms)
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13 pages, 5268 KiB  
Review
Ion Signaling in Cell Motility and Development in Dictyostelium discoideum
by Yusuke V. Morimoto
Biomolecules 2024, 14(7), 830; https://doi.org/10.3390/biom14070830 - 10 Jul 2024
Viewed by 2016
Abstract
Cell-to-cell communication is fundamental to the organization and functionality of multicellular organisms. Intercellular signals orchestrate a variety of cellular responses, including gene expression and protein function changes, and contribute to the integrated functions of individual tissues. Dictyostelium discoideum is a model organism for [...] Read more.
Cell-to-cell communication is fundamental to the organization and functionality of multicellular organisms. Intercellular signals orchestrate a variety of cellular responses, including gene expression and protein function changes, and contribute to the integrated functions of individual tissues. Dictyostelium discoideum is a model organism for cell-to-cell interactions mediated by chemical signals and multicellular formation mechanisms. Upon starvation, D. discoideum cells exhibit coordinated cell aggregation via cyclic adenosine 3′,5′-monophosphate (cAMP) gradients and chemotaxis, which facilitates the unicellular-to-multicellular transition. During this process, the calcium signaling synchronizes with the cAMP signaling. The resulting multicellular body exhibits organized collective migration and ultimately forms a fruiting body. Various signaling molecules, such as ion signals, regulate the spatiotemporal differentiation patterns within multicellular bodies. Understanding cell-to-cell and ion signaling in Dictyostelium provides insight into general multicellular formation and differentiation processes. Exploring cell-to-cell and ion signaling enhances our understanding of the fundamental biological processes related to cell communication, coordination, and differentiation, with wide-ranging implications for developmental biology, evolutionary biology, biomedical research, and synthetic biology. In this review, I discuss the role of ion signaling in cell motility and development in D. discoideum. Full article
(This article belongs to the Special Issue Recent Advances in Supramolecular Motility Machinery of Microorganisms)
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