Updated on 2021/10/21

写真a

 
YOSHIMOTO Shogo
 
Organization
Graduate School of Engineering Biomolecular Engineering 2 Designated assistant professor
Title
Designated assistant professor

Degree 1

  1. Ph.D. ( 2017.3   Nagoya University ) 

Professional Memberships 3

  1. 日本生物工学会

  2. 日本化学会

  3. 化学工学会

 

Papers 10

  1. Single-cell adhesion force mapping of a highly sticky bacterium in liquid Reviewed

    Ishii Satoshi, Yoshimoto Shogo, Hori Katsutoshi

    JOURNAL OF COLLOID AND INTERFACE SCIENCE   Vol. 606 ( Pt 1 ) page: 628 - 634   2022.1

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Journal of Colloid and Interface Science  

    The sticky bacterium Acinetobacter sp. Tol 5 adheres to various material surfaces via its cell surface nanofiber protein, AtaA. This adhesiveness has only been evaluated based on the amount of cells adhering to a surface. In this study, the adhesion force mapping of a single Tol 5 cell in liquid using the quantitative imaging mode of atomic force microscopy (AFM) revealed that the adhesion of Tol 5 was near 2 nN, which was 1–2 orders of magnitude higher than that of other adhesive bacteria. The adhesion force of a cell became stronger with the increase in AtaA molecules present on the cell surface. Many fibers of peritrichate AtaA molecules simultaneously interact with a surface, strongly attaching the cell to the surface. The adhesion force of a Tol 5 cell was drastically reduced in the presence of 1% casamino acids but not in deionized water (DW), although both liquids decrease the adhesiveness of Tol 5 cells, suggesting that DW and casamino acids inhibit the cell approaching step and the subsequent direct interaction step of AtaA with surfaces, respectively. Heterologous production of AtaA provided non-adhesive Acinetobacter baylyi ADP1 cells with a strong adhesion force to AFM tip surfaces of silicon and gold.

    DOI: 10.1016/j.jcis.2021.08.039

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  2. The extracellular juncture domains in the intimin passenger adopt a constitutively extended conformation inducing restraints to its sphere of action Reviewed International coauthorship

    Weikum Julia, Kulakova Alina, Tesei Giulio, Yoshimoto Shogo, Jaegerum Line Vejby, Schuetz Monika, Hori Katsutoshi, Skepo Marie, Harris Pernille, Leo Jack C., Morth J. Preben

    SCIENTIFIC REPORTS   Vol. 10 ( 1 ) page: 21249   2020.12

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Scientific Reports  

    Enterohemorrhagic and enteropathogenic Escherichia coli are among the most important food-borne pathogens, posing a global health threat. The virulence factor intimin is essential for the attachment of pathogenic E. coli to the intestinal host cell. Intimin consists of four extracellular bacterial immunoglobulin-like (Big) domains, D00–D2, extending into the fifth lectin subdomain (D3) that binds to the Tir-receptor on the host cell. Here, we present the crystal structures of the elusive D00–D0 domains at 1.5 Å and D0–D1 at 1.8 Å resolution, which confirms that the passenger of intimin has five distinct domains. We describe that D00–D0 exhibits a higher degree of rigidity and D00 likely functions as a juncture domain at the outer membrane-extracellular medium interface. We conclude that D00 is a unique Big domain with a specific topology likely found in a broad range of other inverse autotransporters. The accumulated data allows us to model the complete passenger of intimin and propose functionality to the Big domains, D00–D0–D1, extending directly from the membrane.

    DOI: 10.1038/s41598-020-77706-7

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  3. Native display of a huge homotrimeric protein fiber on the cell surface after precise domain deletion Reviewed International coauthorship

    Aoki Sota, Yoshimoto Shogo, Ishikawa Masahito, Linke Dirk, Lupas Andrei, Hori Katsutoshi

    JOURNAL OF BIOSCIENCE AND BIOENGINEERING   Vol. 129 ( 4 ) page: 412 - 417   2020.4

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Journal of Bioscience and Bioengineering  

    AtaA, a trimeric autotransporter adhesin from Acinetobacter sp. Tol 5, exhibits nonspecific, high adhesiveness to abiotic surfaces. For identification of the functional domains of AtaA, precise design of domain-deletion mutants is necessary so as not to cause undesirable structural distortion. Here, we designed and constructed three types of AtaA mutants from which the same domain, FGG1, was deleted. The first mutant was designed to preserve the periodicity of hydrophobic residues in the coiled-coil segments sandwiching the deleted region. After the deletion, the protein was properly displayed on the cell surface and had the same adhesive function as the wild type. Transmission electron microscopy (TEM) imaging and circular dichroism (CD) spectroscopy showed that its isolated passenger domain had the same fiber structure as in the AtaA wild type. In contrast, a mutant designed to disturb the coiled-coil periodicity at the deletion site failed to reach the cell surface. Although secretion occurred for the mutant designed with a flexible connector between the coiled coils, the cells exhibited a decrease in adhesiveness. Furthermore, TEM imaging of the mutant fibers showed bending at the fiber tip and changes in their CD spectrum indicated a decrease in secondary structure content. Thus, we succeeded to natively display the huge homotrimeric fiber structure of AtaA on the cell surface after precise deletion of a domain, maintaining the proper folding state and adhesive function by preserving its coiled-coil periodicity. This strategy enables us to construct various domain-deletion mutants of AtaA without structural distortion for complete functional mapping.

    DOI: 10.1016/j.jbiosc.2019.09.022

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  4. Process Description of an Unconventional Biofilm Formation by Bacterial Cells Autoagglutinating through Sticky, Long, and Peritrichate Nanofibers Reviewed

    Furuichi Yoshihide, Yoshimoto Shogo, Inaba Tomohiro, Nomura Nobuhiko, Hori Katsutoshi

    ENVIRONMENTAL SCIENCE & TECHNOLOGY   Vol. 54 ( 4 ) page: 2520 - 2529   2020.2

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Environmental Science and Technology  

    In this study, we elucidated the formation process of an unconventional biofilm formed by a bacterium autoagglutinating through sticky, long, and peritrichate nanofibers. Understanding the mechanisms of biofilm formation is essential to control microbial behavior and improve environmental biotechnologies. Acinetobacter sp. Tol 5 autoagglutinate through the interaction of the long, peritrichate nanofiber protein AtaA, a trimeric autotransporter adhesin. Using AtaA, without cell growth or extracellular polymeric substances production, Tol 5 cells quickly form an unconventional biofilm. The process forming this unconventional biofilm started with cell-cell interactions, proceeded to cell clumping, and led to the formation of large cell aggregates. The cell-cell interaction was described by Derjaguin-Landau-Verwey-Overbeek (DLVO) theory based on a new concept, which considers two independent interactions between two cell bodies and between two AtaA fiber tips forming a discontinuous surface. If cell bodies cannot collide owing to an energy barrier at low ionic strengths but approach within the interactive distance of AtaA fibers, cells can agglutinate through their contact. Cell clumping proceeds following the cluster-cluster aggregation model, and an unconventional biofilm containing void spaces and a fractal nature develops. Understanding its formation process would extend the utilization of various types of biofilms, enhancing environmental biotechnologies.

    DOI: 10.1021/acs.est.9b06577

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  5. Bottom-up Creation of an Artificial Cell Covered with the Adhesive Bacterionanofiber Protein AtaA Reviewed

    Noba Kosaku, Ishikawa Masahito, Uyeda Atsuko, Watanabe Takayoshi, Hohsaka Takahiro, Yoshimoto Shogo, Matsuura Tomoaki, Hori Katsutoshi

    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY   Vol. 141 ( 48 ) page: 19058 - 19066   2019.12

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Journal of the American Chemical Society  

    The bacterial cell surface structure has important roles for various cellular functions. However, research on reconstituting bacterial cell surface structures is limited. This study aimed to bottom-up create a cell-sized liposome covered with AtaA, the adhesive bacterionanofiber protein localized on the cell surface of Acinetobacter sp. Tol 5, without the use of the protein secretion and assembly machineries. Liposomes containing a benzylguanine derivative-modified phospholipid were decorated with a truncated AtaA protein fused to a SNAP-tag expressed in a soluble fraction in Escherichia coli. The obtained liposome showed a similar surface structure and function to that of native Tol 5 cells and adhered to both hydrophobic and hydrophilic solid surfaces. Furthermore, this artificial cell was able to drive an enzymatic reaction in the adhesive state. The developed artificial cellular system will allow for analysis of not only AtaA, but also other cell surface proteins under a cell-mimicking environment. In addition, AtaA-decorated artificial cells may inspire the development of biotechnological applications that require immobilization of cells onto a variety of solid surfaces, in particular, in environments where the use of genetically modified organisms is prohibited.

    DOI: 10.1021/jacs.9b09340

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  6. Control of AtaA-mediated bacterial immobilization by casein hydrolysates Reviewed

    Ohara Yuki, Yoshimoto Shogo, Hori Katsutoshi

    JOURNAL OF BIOSCIENCE AND BIOENGINEERING   Vol. 128 ( 5 ) page: 544 - 550   2019.11

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Journal of Bioscience and Bioengineering  

    Acinetobacter sp. Tol 5 exhibits an autoagglutinating nature and high adhesiveness to various abiotic surfaces through its bacterionanofiber protein AtaA. We have developed new bacterial immobilization methods utilizing the high adhesiveness of AtaA. We previously reported that salt is essential for the adhesiveness of AtaA. In the current study, we unexpectedly found that Tol 5 cells were not immobilized onto polyurethane foam support during growth in LB medium although AtaA was properly expressed and displayed onto the cell surface. The adhesion of Tol 5 resting cells was not affected by sugars but drastically inhibited by yeast extract and casein hydrolysates such as tryptone and casamino acids technical grade (CA-T). Some amino acids, which are major components of CA-T, partially inhibited the adhesion of Tol 5 cells. Experimental results suggested that oligopeptides might effectively inhibit the cell adhesion. Immobilized cells onto the support through AtaA were detached in CA-T solution. Also, the detached cells could be re-immobilized onto the support without impairing of their adhesiveness by replacing CA-T solution to a basal salt medium. Microscopic observation revealed that breaking of AtaA-mediated cell–cell interaction is important for the detachment of Tol 5 cells from the support. CA-T also inhibited AtaA-mediated autoagglutination and dispersed cell clumps through AtaA. This is the first report on adhesion inhibitors against AtaA and suggests that casein hydrolysates like CA-T would be a powerful tool for controlling AtaA-mediated bacterial immobilization.

    DOI: 10.1016/j.jbiosc.2019.04.019

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  7. Reversible bacterial immobilization based on the salt-dependent adhesion of the bacterionanofiber protein AtaA Reviewed

    Yoshimoto Shogo, Ohara Yuki, Nakatani Hajime, Hori Katsutoshi

    MICROBIAL CELL FACTORIES   Vol. 16 ( 1 ) page: 123   2017.7

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    Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:Microbial Cell Factories  

    Background: Immobilization of microbial cells is an important strategy for the efficient use of whole-cell catalysts because it simplifies product separation, enables the cell concentration to be increased, stabilizes enzymatic activity, and permits repeated or continuous biocatalyst use. However, conventional immobilization methods have practical limitations, such as limited mass transfer in the inner part of a gel, gel fragility, cell leakage from the support matrix, and adverse effects on cell viability and catalytic activity. We previously showed a new method for bacterial cell immobilization using AtaA, a member of the trimeric autotransporter adhesin family found in Acinetobacter sp. Tol 5. This approach is expected to solve the drawbacks of conventional immobilization methods. However, similar to all other immobilization methods, the use of support materials increases the cost of bioprocesses and subsequent waste materials. Results: We found that the stickiness of the AtaA molecule isolated from Tol 5 cells is drastically diminished at ionic strengths lower than 10 mM and that it cannot adhere in deionized water, which also inhibits cell adhesion mediated by AtaA. Cells immobilized on well plates and polyurethane foam in a salt solution were detached in deionized water by rinsing and shaking, respectively. The detached cells regained their adhesiveness in a salt solution and could rapidly be re-immobilized. The cells expressing the ataA gene maintained their adhesiveness throughout four repeated immobilization and detachment cycles and could be repeatedly immobilized to polyurethane foam by a 10-min shake in a flask. We also demonstrated that both bacterial cells and a support used in a reaction could be reused for a different type of reaction after detachment of the initially immobilized cells from the support and a subsequent immobilization step. Conclusions: We invented a unique reversible immobilization method based on the salt-dependent adhesion of the AtaA molecule that allows us to reuse bacterial cells and supports by a simple manipulation involving a deionized water wash. This mitigates problems caused by the use of support materials and greatly helps to enhance the efficiency and productivity of microbial production processes.

    DOI: 10.1186/s12934-017-0740-7

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  8. Secretion of the Intimin Passenger Domain Is Driven by Protein Folding Reviewed International coauthorship

    Leo Jack C., Oberhettinger Philipp, Yoshimoto Shogo, Udatha D. B. R. K. Gupta, Morth J. Preben, Schuetz Monika, Hori Katsutoshi, Linke Dirk

    JOURNAL OF BIOLOGICAL CHEMISTRY   Vol. 291 ( 38 ) page: 20096 - 20112   2016.9

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Journal of Biological Chemistry  

    Intimin is an essential adhesin of attaching and effacing organisms such as entropathogenic Escherichia coli. It is also the prototype of type Ve secretion or inverse autotransport, where the extracellular C-terminal region or passenger is exported with the help of an N-terminal transmembrane β-barrel domain. We recently reported a stalled secretion intermediate of intimin, where the passenger is located in the periplasm but the β-barrel is already inserted into the membrane. Stalling of this mutant is due to the insertion of an epitope tag at the very N terminus of the passenger. Here, we examined how this insertion disrupts autotransport and found that it causes misfolding of the N-terminal immunoglobulin (Ig)-like domain D00. We could also stall the secretion by making an internal deletion in D00, and introducing the epitope tag into the second Ig-like domain, D0, also resulted in reduced passenger secretion. In contrast to many classical autotransporters, where a proximal folding core in the passenger is required for secretion, the D00 domain is dispensable, as the passenger of an intimin mutant lacking D00 entirely is efficiently exported. Furthermore, the D00 domain is slightly less stable than the D0 and D1 domains, unfolding at ∼200 piconewtons (pN) compared with ∼250 pN for D0 and D1 domains as measured by atomic force microscopy. Our results support a model where the secretion of the passenger is driven by sequential folding of the extracellular Ig-like domains, leading to vectorial transport of the passenger domain across the outer membrane in an N to C direction.

    DOI: 10.1074/jbc.M116.731497

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  9. Discovery of a novel periplasmic protein that forms a complex with a trimeric autotransporter adhesin and peptidoglycan Reviewed

    Ishikawa Masahito, Yoshimoto Shogo, Hayashi Ayumi, Kanie Junichi, Hori Katsutoshi

    MOLECULAR MICROBIOLOGY   Vol. 101 ( 3 ) page: 394 - 410   2016.8

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Molecular Microbiology  

    Trimeric autotransporter adhesins (TAAs), fibrous proteins on the cell surface of Gram-negative bacteria, have attracted attention as virulence factors. However, little is known about the mechanism of their biogenesis. AtaA, a TAA of Acinetobacter sp. Tol 5, confers nonspecific, high adhesiveness to bacterial cells. We identified a new gene, tpgA, which forms a single operon with ataA and encodes a protein comprising two conserved protein domains identified by Pfam: an N-terminal SmpA/OmlA domain and a C-terminal OmpA_C-like domain with a peptidoglycan (PGN)-binding motif. Cell fractionation and a pull-down assay showed that TpgA forms a complex with AtaA, anchoring it to the outer membrane (OM). Isolation of total PGN-associated proteins showed TpgA binding to PGN. Disruption of tpgA significantly decreased the adhesiveness of Tol 5 because of a decrease in surface-displayed AtaA, suggesting TpgA involvement in AtaA secretion. This is reminiscent of SadB, which functions as a specific chaperone for SadA, a TAA in Salmonella species; however, SadB anchors to the inner membrane, whereas TpgA anchors to the OM through AtaA. The genetic organization encoding the TAA–TpgA-like protein cassette can be found in diverse Gram-negative bacteria, suggesting a common contribution of TpgA homologues to TAA biogenesis.

    DOI: 10.1111/mmi.13398

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  10. An Acinetobacter trimeric autotransporter adhesin reaped from cells exhibits its nonspecific stickiness via a highly stable 3D structure Reviewed

    Yoshimoto Shogo, Nakatani Hajime, Iwasaki Keita, Hori Katsutoshi

    SCIENTIFIC REPORTS   Vol. 6   page: 28020   2016.6

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Scientific Reports  

    Trimeric autotransporter adhesins (TAAs), cell surface proteins of Gram-negative bacteria, mediate bacterial adhesion to host cells and extracellular matrix proteins. However, AtaA, a TAA in the nonpathogenic Acinetobacter sp. strain Tol 5, shows nonspecific, high adhesiveness to abiotic material surfaces as well as to biotic surfaces. AtaA is a homotrimer of polypeptides comprising 3,630 amino acids and forms long nanofibers; therefore, it is too large and structurally complex to be produced as a recombinant protein. In this study, we isolated AtaA's passenger domain (AtaA PSD), which is translocated to the cell surface through the C-terminal transmembrane domain and exhibits biological functions, using a new method. We introduced a protease recognition site and reaped AtaA nanofibers 225 nm in length from the cell surface through proteolytic cleavage with a specific protease. Biochemical and biophysical analyses of the purified native AtaA PSD revealed that it has a stable structure under alkaline and acidic conditions. Temperatures above 80 °C, which disrupted AtaA's higher-order structure but maintained the full-length AtaA polypeptide, inactivated AtaA's nonspecific adhesiveness, suggesting that the stickiness of AtaA requires its 3D structure. This finding refutes the widespread but vague speculation that large unfolded polypeptides readily stick to various surfaces.

    DOI: 10.1038/srep28020

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Research Project for Joint Research, Competitive Funding, etc. 1

  1. 固相基質分解酵素複合体の分子設計基盤の確立

    Grant number:JPMJAX20BL  2020.12 - 2023.3

    JST  ACT-X 

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    Authorship:Principal investigator 

KAKENHI (Grants-in-Aid for Scientific Research) 2

  1. ナノファイバータンパク質AtaAの粘弾性発現機構解明

    Grant number:20K15098  2020.4 - 2022.3

    科学研究費助成事業   若手研究

    吉本 将悟

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    Authorship:Principal investigator 

    Grant amount:\4290000 ( Direct Cost: \3300000 、 Indirect Cost:\990000 )

    アシネトバクター属細菌由来のナノファイバータンパク質AtaAは、プラスチック、ガラス、金属など様々な材料表面に対し水中で高い接着性を示すため、新規のバイオ材料固定化マテリアルとして期待される。最近、AtaAが他のタンパク質とは異なるユニークな粘弾性を示すことが分かってきた。本研究では、AtaAの粘弾性がどのようにして発揮されるのかを、原子間力顕微鏡を用いた解析と計算により分子レベルで明らかにする。

  2. 材料非特異接着タンパク質AtaAの接着機構の理解

    Grant number:18K14062  2018.4 - 2020.3

    科学研究費助成事業  若手研究

    吉本 将悟

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    Authorship:Principal investigator 

    Grant amount:\4160000 ( Direct Cost: \3200000 、 Indirect Cost:\960000 )