Tomoko Miyata

ORCID: 0000-0002-5543-7459
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About
Contact & Profiles
Research Areas
  • Bacterial Genetics and Biotechnology
  • Microtubule and mitosis dynamics
  • Bacteriophages and microbial interactions
  • Advanced Electron Microscopy Techniques and Applications
  • Enzyme Structure and Function
  • Photosynthetic Processes and Mechanisms
  • DNA Repair Mechanisms
  • ATP Synthase and ATPases Research
  • RNA and protein synthesis mechanisms
  • Lipid Membrane Structure and Behavior
  • Protist diversity and phylogeny
  • RNA modifications and cancer
  • Micro and Nano Robotics
  • Electrochemical sensors and biosensors
  • Nuclear Structure and Function
  • Metalloenzymes and iron-sulfur proteins
  • CO2 Reduction Techniques and Catalysts
  • Amino Acid Enzymes and Metabolism
  • Advanced biosensing and bioanalysis techniques
  • Epigenetics and DNA Methylation
  • Genomics and Phylogenetic Studies
  • RNA Research and Splicing
  • DNA and Nucleic Acid Chemistry
  • T-cell and Retrovirus Studies
  • Protein Structure and Dynamics

Osaka University
2016-2025

University of Osijek
2024

Ube Frontier University
2006-2022

Suita Municipal Hospital
2022

Osaka Hospital
2022

Scripps Research Institute
2017

National Center For Child Health and Development
2014-2015

Kyushu University
1981-2015

Nagoya University Hospital
1994-2014

Aichi Cancer Center
2009-2014

Rotary ATPases, including F 1 O -, V and A -ATPases, are molecular motors that exhibit rotational movements for energy conversion. In the gliding bacterium, Mycoplasma mobile , a dimeric -like ATPase forms chain structure within cell, which is proposed to drive motility. However, mechanisms of force generation transmission remain unclear. We determined electron cryomicroscopy (cryo-EM) complex. The revealed an assembly distinct from those -ATPases. unit associated by two subunits GliD GliE...

10.1126/sciadv.adr9319 article EN cc-by-nc Science Advances 2025-02-26

The flagellar MS-ring is the initial template for assembly and houses protein export complex. has three parts of different symmetries within ring structure by FliF subunits in two conformations with distinct arrangements ring-building motifs, RBM1, RBM2, RBM3. However, it remains unknown how these are generated. A combination cryoEM structure-based mutational analyses demonstrates that well-conserved DQxGxxL motif RBM2-RBM3 hinge loop allows RBM2 to take orientations relative Of 34 basal...

10.1038/s42003-025-07485-2 article EN cc-by-nc-nd Communications Biology 2025-01-16

10.1107/s0567740880002981 article EN Acta Crystallographica Section B 1980-02-01

beta-2-Microglobulin (beta-2m) is a major constituent of amyloid fibrils in patients with dialysis-related amyloidosis (DRA). Recently, we found that the pigmented and fluorescent adducts formed nonenzymatically between sugar protein, known as advanced glycation end products (AGEs), were present beta-2m-containing fibrils, suggesting possible involvement AGE-modified beta-2m bone joint destruction DRA. As an extension our search for native structure AGEs DRA, study focused on pentosidine,...

10.1073/pnas.93.6.2353 article EN Proceedings of the National Academy of Sciences 1996-03-19

Bacterial pathogens use an injectisome to deliver virulence proteins into eukaryotic host cells. The bacterial flagellum and export their component for self-assembly. These two systems show high structural similarities are classified as the type III secretion system, but it remains elusive how similar they in situ because structures of these complexes isolated from cells visualized by electron cryomicroscopy have shown only channel housing apparatus. Here we report Salmonella cryotomography....

10.1038/srep03369 article EN cc-by-nc-nd Scientific Reports 2013-11-28

Ring-shaped sliding clamps and clamp loader ATPases are essential factors for rapid accurate DNA replication. The ring is opened resealed at the primer–template junctions by ATP-fueled function. processivity of polymerase conferred its attachment to loaded onto DNA. In eukarya archaea, replication factor C (RFC) proliferating cell nuclear antigen (PCNA) play crucial roles as clamp, respectively. Here, we report electron microscopic structure an archaeal RFC–PCNA–DNA complex 12-Å resolution....

10.1073/pnas.0506447102 article EN Proceedings of the National Academy of Sciences 2005-09-16

Smart health care, that measures users' living conditions and status using small sensing devices collecting their data over a network under daily life, is expected as new trend. It getting paid more attention along with the increase of demands preventive care. In this paper, vital rates amount accumulation in variety smart care use cases are discussed. Then, relationship between possible applications short-range wireless systems Finally, our developed patch type wearable monitoring device...

10.1109/ismict.2013.6521687 article EN 2013-03-01

Abstract A photofunctionalized square bipyramidal DNA nanocapsule (NC) was designed and prepared for the creation of a nanomaterial carrier. Photocontrollable open/close system toehold were introduced into NC inclusion release gold nanoparticle (AuNP) by photoirradiation strand displacement. The reversible open closed states examined gel electrophoresis atomic force microscopy (AFM), behavior directly observed high‐speed AFM. encapsulation DNA‐modified AuNP within carried out hybridization...

10.1002/chem.201404757 article EN Chemistry - A European Journal 2014-09-15

Abstract The bacterial flagellum is a motile organelle driven by rotary motor, and its axial portions function as drive shaft (rod), universal joint (hook) helical propeller (filament). rod hook are directly connected to each other, with their subunit proteins FlgG FlgE having 39% sequence identity, but show distinct mechanical properties; the straight rigid whereas flexible in bending joint. Here we report structure of comparison that hook. While these two structures have same symmetry...

10.1038/ncomms14276 article EN cc-by Nature Communications 2017-01-25

The bacterial flagellum is a motility organelle consisting of long helical filament as propeller and rotary motor that drives rapid rotation to produce thrust. Salmonella enterica serovar Typhimurium has two genes flagellin, fljB fliC, for flagellar formation autonomously switches their expression at frequency 10−3–10−4 per cell generation. We report here differences in structures functions under high-viscosity conditions. A strain expressing FljB showed higher than one FliC high viscosity....

10.3390/biom10020246 article EN cc-by Biomolecules 2020-02-06

Abstract The bacterial flagellar MS ring is a transmembrane complex acting as the core of motor and template for assembly. C attached to involved in torque generation rotation switch, large symmetry mismatch between these two rings has been long puzzle, especially with respect their role function. Here, using cryoEM structural analysis basal body formed by full-length FliF from Salmonella enterica , we show that native 34 subunits no variation. Symmetry shows variation peak at 34-fold,...

10.1038/s41467-021-24507-9 article EN cc-by Nature Communications 2021-07-09

Abstract The basal body of the bacterial flagellum is a rotary motor that consists several rings (C, MS and LP) rod. LP ring acts as bushing supporting distal rod for its rapid stable rotation without much friction. Here, we use electron cryomicroscopy to describe structure around rod, at 3.5 Å resolution, from Salmonella Typhimurium. shows 26-fold rotational symmetry intricate intersubunit interactions each subunit with up six partners, which explains structural stability. inner surface...

10.1038/s41467-021-24715-3 article EN cc-by Nature Communications 2021-07-22

RecA and Rad51 proteins are essential for homologous recombination in <i>Bacteria</i> and<i>Eukarya</i>, respectively. Homologous proteins, called RadA, have been described <i>Archaea</i>. Here we present the characterization of two RecA/Rad51 family RadA RadB, from<i>Pyrococcus furiosus</i>. The <i>radA</i> and<i>radB</i> genes were not induced by DNA damage resulting from exposure cells to γ UV irradiation heat shock, suggesting that they might be constitutively expressed this...

10.1074/jbc.m004557200 article EN cc-by Journal of Biological Chemistry 2000-10-01

In bacteria, 70S ribosomes (consisting of 30S and 50S subunits) dimerize to form 100S ribosomes, which were first discovered in E scherichia coli . Ribosome modulation factor ( RMF ) hibernation promoting HPF mediate this dimerization stationary phase. The 100 S ribosome is translationally inactive, but it dissociates into two active 70 after transfer from starvation fresh medium. Therefore, the called ‘hibernating ribosome’. gene encoding found widely throughout G ammaproteobacteria class,...

10.1111/gtc.12057 article EN Genes to Cells 2013-05-13

The V1- and F1- rotary ATPases contain a rotor that rotates against catalytic A3B3 or α3β3 stator. F1-γ V1-DF is composed of both anti-parallel coiled coil globular-loop parts. bacterial flagellar type III export apparatus contains V1/F1-like ATPase ring structure FliI6 homo-hexamer FliJ which adopts an without the part. Here we report Salmonella enterica serovar Typhimurium shows like function in Thermus thermophilus based on biochemical structural analysis. Single molecular analysis...

10.1371/journal.pone.0064695 article EN cc-by PLoS ONE 2013-05-28

The efficient utilization of biomass fuels is a critical component sustainable energy economy. Via respiration, acetic acid bacteria can oxidize ethanol into using membrane-bound alcohol and aldehyde dehydrogenases (ADH AlDH, respectively). Focusing on the ability these enzymes to interact directly electrically with electrode materials, we constructed mediatorless bioanode for oxidation based direct electron transfer (DET)-type bienzymatic cascade by ADH AlDH. three-dimensional structural...

10.1021/acscatal.3c01962 article EN ACS Catalysis 2023-05-30

Photosynthetic inefficiencies limit the productivity and sustainability of crop production resilience agriculture to future societal environmental challenges. Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) has inherently low catalytic efficiency, making it a key target for photosynthesis improvement. However, introducing mutations chloroplast-encoded Rubisco large subunit (rbcL), which contains enzyme's sites, is technically challenging. In this study, we successfully generated...

10.1101/2025.01.02.631008 preprint EN cc-by-nc bioRxiv (Cold Spring Harbor Laboratory) 2025-01-03

The FliPQR complex constitutes a channel for export of the bacterial flagellar proteins involved in axial structure assembly. It also serves as template rod A periplasmic gate, formed by N-terminal α-helices FliP and FliR, remains closed until FliE assembles onto FliR. mechanism which opens gate has remained unclear. Here, we present cryoEM form at 3.0 Å resolution. β-cap β-strands FliR creates tight seal gate. Interaction with induces conformational change their move up outward....

10.1101/2025.02.07.637169 preprint EN cc-by bioRxiv (Cold Spring Harbor Laboratory) 2025-02-08

Abstract Biparatopic antibodies (BpAbs) bind two different antigen epitopes to form characteristic immunocomplexes. Many BpAbs have been developed for enhanced cross-linking induce signal transduction or cell internalization, whereas few were reported with smaller immunocomplexes suppress unwanted signaling. Here, we a strategy 1:1 immunocomplex formation maximize antagonistic function. Various peptide linkers introduced into the hinge regions of IgG-like agonist against tumor necrosis...

10.1101/2025.02.11.637430 preprint EN cc-by-nc bioRxiv (Cold Spring Harbor Laboratory) 2025-02-15

Mycoplasma pneumoniae and genitalium are bacterial wall-less human pathogens the causative agents of respiratory reproductive tract infections. Infectivity, gliding motility adhesion these mycoplasmas to host cells mediated by orthologous adhesin proteins forming a transmembrane complex that binds sialylated oligosaccharides cell ligands. Here we report cryo-EM structure M. P1 bound Fab fragment monoclonal antibody P1/MCA4, which stops induces detachment motile cells. The epitope P1/MCA4...

10.1371/journal.ppat.1012973 article EN cc-by PLoS Pathogens 2025-03-28

Inositol 1,4,5-trisphosphate receptor (IP<sub>3</sub>R) is a highly controlled calcium (Ca<sup>2+</sup>) channel gated by inositol (IP<sub>3</sub>). Multiple regulators modulate IP<sub>3</sub>-triggered pore opening binding to discrete allosteric sites within IP<sub>3</sub>R. Accordingly we have postulated that these structurally control ligand gating behavior; however, no structural evidence has been available. Here show Ca<sup>2+</sup>, the most pivotal regulator, induced marked changes in...

10.1074/jbc.c200244200 article EN cc-by Journal of Biological Chemistry 2002-06-01

ABSTRACT Bacterial flagella play key roles in surface attachment and host-bacterial interactions as well driving motility. Here, we have investigated the ability of Caulobacter crescentus to assemble its flagellar filament from six flagellins: FljJ, FljK, FljL, FljM, FljN, FljO. Flagellin gene deletion combinations exhibited a range phenotypes no motility or impaired full Characterization mutant collection showed following: (i) that there is strict requirement for any one flagellins...

10.1128/jb.01172-10 article EN Journal of Bacteriology 2011-03-27
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