Biology subjects

Kiyama, H.

Publications and source records attributed to Kiyama, H..

7 recordsLinked to original sources

bioRxiv2026

Reconstitution in a minimal synthetic bacterium reveals distinct Mollicute MreB-based motility systems driven by orthogonal force directions

MreB, a bacterial actin homolog, is widely conserved in bacteria where it functions as a scaffold for a peptidoglycan synthesis. Intriguingly, members of the cell wall-lacking Mollicutes retain multiple mreB genes despite the absence of peptidoglycan. Previous work demonstrated that two MreB isoforms from Spiroplasma can reconstitute swimming motility in the minimal synthetic bacterium syn3B, indicating that MreB was repurposed for motility. Here, we expressed seven MreBs from Haloplasma contractile, an early-diverging Mollicute, in syn3B. Approximately 50% of cells elongated, and 15% exhibited curving and coiling movements that resembled Haloplasma but differed from Spiroplasma motility. Systematic analysis of isoform combinations revealed that movement requires specific MreB pairs, and that additional isoforms enhance motility efficiency. Cryo-electron tomography showed membrane-associated ribbons composed of MreB filaments. Mathematical modeling demonstrated that Haloplasma- and Spiroplasma-type movements can be reproduced by altering only the direction of force generation. Thus, diversification of force orientation within an actin homolog enabled independent evolution of distinct motility systems in Mollicutes.

Synthetic Biology↗

bioRxiv2026

Coordinated Membrane Deformation Driven by a Minimal Set of Spiroplasma MreB Isoforms

Spiroplasma are wall-less helical bacteria that swim by switching the handedness of their helices. In most bacteria, MreB, a bacterial actin, forms relatively static filaments beneath the membrane to organize cell wall synthesis. In contrast, Spiroplasma eriocheiris encodes five MreB isoforms (SpeMreBs), and swimming requires a pair of isoforms, SpeMreB5 together with SpeMreB4 (or the related isoform SpeMreB1) (1) Yet how these MreBs generate force and membrane deformation remains unclear. To examine the membrane-deforming activities of SpeMreBs, we demonstrated a simple reconstitution system using the non-motile synthetic bacterium JCVI-syn3B and purified SpeMreBs expressed in Escherichia coli. Lysates of syn3B expressing SpeMreB5 deformed liposomes in a concentration-dependent manner. In contrast, lysates co-expressing both SpeMreB5 and SpeMreB4 showed a plateau in the frequency of deformation, suggesting that SpeMreB4 suppresses membrane deformation driven by SpeMreB5. Deformed liposomes exhibited either fluctuating or stable behaviors. ATP depletion changed both the frequency and behavior of deformation, indicating that membrane remodeling depends on the nucleotide state of SpeMreBs. Reconstitution with purified SpeMreBs from E. coli confirmed that SpeMreB5 alone deforms membranes, whereas SpeMreB1, a member of the same class as SpeMreB4, suppresses deformation. These results suggest that membrane shape in Spiroplasma is dynamically regulated by antagonistic interactions among isoforms of SpeMreBs isoforms and their nucleotide-dependent assembly states.

synthetic biology↗

bioRxiv2025

Live imaging of bacterial actin MreBs causing helicity switching of a minimal synthetic cell

Spiroplasma swim by switching their helical body into right- and left-handed. Helicity formation and switching can be reconstituted in an immotile minimal synthetic bacterium, JCVI-syn3B by introducing the pair of bacterial actin, MreB4 and MreB5. Here, we analyzed MreB behaviors optically, to investigate this unknown mechanism. We tried MreB4 fluorescence labeling by protein fusion. The labeling was not achieved, because the fusion of fluorescent protein or peptide to 16 positions resulted in immotile constructs. These results may suggest that MreB4 has many interaction interfaces with other proteins. Induced expression of MreB4 to cells with constitutive MreB5 expression resulted in earlier and higher frequency of motile cells, distinct from the results of constitutive MreB4 and inducible MreB5. Next, the behavior of labeled MreB5 was analyzed. Photobleaching and photoactivation suggested static behavior of MreB5 during cell movements. Cell treatment by A22, a MreB polymerization inhibitor caused helix deformation, movement stall, and diffusion of MreB5 fluorescence, suggesting that A22 sensitive MreB5 interaction should be involved in helix formation and motility. SignificanceSpiroplasma MreB is a unique bacterial actin that causes motility with a different mechanism from other actins. Here, we investigated the helicity switching involved in the motility. Fluorescently traced MreB behaviors suggested that the motility mechanism is not coupled with its replacement in the internal structure.

biophysics↗

bioRxiv2024

A highly active bacterial actin actuates the polymerization of another isoform essential for swimming motility of Spiroplasma

Spiroplasma is a wall-less helical bacterium that is characterized by a unique swimming motility involving five isoforms of the bacterial actin MreBs (SMreB1-5). The functions of SMreBs are unique in the MreB family proteins, as their counterparts in walled-bacteria are involved in maintaining the cell shape by scaffolding the cell-wall synthesis complex through their static properties. In vitro analyses of individual SMreBs provide clues to understand the detailed molecular mechanism of Spiroplasma swimming. However, the purification difficulties have hampered in vitro analyses of one of the SMreBs, SMreB1, which drives the swimming. Here, we isolated soluble SMreB1 of Spiroplasma eriocheiris (SpeMreB1) and evaluated its activity. SpeMreB1 was expressed as a fusion with a solubilization-tag, ProteinS (PrS), which allowed us to purify it in the soluble fraction. SpeMreB1 exhibited the highest phosphate release rate and the fold changes of critical concentrations for polymerization across the nucleotide states among the MreB family proteins. SpeMreB1 interacted with polymerized SpeMreB5, another SMreB essential for Spiroplasma swimming. In the AMPPNP- or ADP-bound state, SpeMreB1 decreased the amount of SpeMreB5 filaments, possibly reflecting their disassembly. Regardless of the nucleotide state, SpeMreB1 bound to negatively charged lipids. These results suggest that SpeMreB1 utilizes its highest activity to manage SpeMreB5 filaments underneath the cell membrane to drive Spiroplasma swimming. ImportanceIn most bacterial species, MreB is involved in cell-shape maintenance by localizing the bacterial cell-wall synthesis complex with its static properties. In contrast, five isoforms of MreBs in a pathogenic wall-less helical bacterium Spiroplasma are involved in its unique motility system driven by a kink propagation along the helical cell. Our integrated biochemical assays show that one isoform of MreBs involved in the swimming of a crustacean pathogen S. eriocheiris (SpeMreB1) is exceptionally active in the MreB family proteins and manages the polymerization of another MreB essential for the swimming (SpeMreB5). This study sheds light on an evolutionary mystery how Spiroplasma has adapted static MreB proteins to a dynamic phenomenon like its swimming motility.

biophysics↗

bioRxiv2024

Establishment of a rapid method to assemble and transfer DNA fragments into the JCVI-syn3B minimal synthetic bacterial genome

JCVI-syn3B (syn3B), a minimal synthetic bacterium that only possesses essential genes, facilitates the examination of heterogeneous gene functions in minimal life. Conventionally, Escherichia coli is used to construct DNA fragments for gene transfer into the syn3B genome through Cre/loxP system. However, the construction process is challenging and time-consuming due to various issues, including the inhibition of E. coli growth and unexpected recombination, especially with AT-rich DNA sequences such as those found in Mycoplasma genes. Therefore, in this study, we aimed to develop a new transformation method to overcome these issues. We assembled the vector and target DNA fragments using an in vitro homologous recombination system and subsequently transferred the products into the syn3B genome. We obtained approximately 103[~]104 recombinant colonies per milliliter of the original culture in eight days, which is four days shorter than the conventional period, without any recombination issues, even for AT-rich DNA. This method may be applicable to other gene manipulation systems based on Cre/loxP system. SignificanceA rapid and trouble free method was developed to transfer genes to the genome of minimal synthetic bacterium JCVI-Syn3B through Cre/loxP system. This method can be applied to Cre/loxP-based gene manipulation system in various research fields.

synthetic biology↗

bioRxiv2023

Cryo-EM of cytoskeletal 'fibril' protein involved in Spiroplasma swimming

Spiroplasma, parasitic or commensal bacteria, can swim by switching the handedness of its helical cell body. A helical cell body is formed by an internal ribbon of MreB, an actin superfamily, and Spiroplasma-specific fibril proteins. Here we have solved the structure of the fibril filament by single-particle cryo-electron microscopy at 3.6 [A] resolution and built its atomic structure. The structure is composed of repeated rings and cylinders. The N-terminal cylinder of the fibril protein shows a structure similar to that of S-adenosylhomocysteine nucleosidase, while the C-terminal ring does not show similarity to other proteins. The filament is nonpolar and flexible, possessing a helical pitch of 700 nm, consistent with cell helicity. Cryo-electron tomography revealed aligned several MreB filaments in the center of the ribbon, flanked by membrane-binding fibril filaments through electrostatic interactions. This study discusses the evolution and roles of the fibril filament.

microbiology↗

bioRxiv2021

Reconstitution of Spiroplasma swimming by expressing two bacterial actins in synthetic minimal bacterium

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, non-motile minimal bacterium, JCVI-syn3.0B, whose reduced genome was computer-designed and chemically synthesized. The synthetic bacterium exhibited swimming motility with features characteristic of Spiroplasma swimming. Moreover, some combinations of the two proteins produced a helical cell shape and swimming, suggesting that the swimming originated from the differentiation and coupling of bacterial actins, and we also obtained a minimal system for motility of the synthetic bacterium. One-Sentence SummaryThe minimal system comprised two bacterial actins that provided cell helicity and swimming to the synthetic minimal bacterium.

synthetic biology↗