Updated on 2024/07/14

写真a

 
SEKI, Takahiro
 
Affiliation
Faculty of Science and Engineering, Waseda Research Institute for Science and Engineering
Job title
Junior Researcher(Assistant Professor)
 

Papers

  • ABCF ATPases Involved in Protein Synthesis, Ribosome Assembly and Antibiotic Resistance: Structural and Functional Diversification across the Tree of Life.

    Victoriia Murina, Marje Kasari, Hiraku Takada, Mariliis Hinnu, Chayan Kumar Saha, James W Grimshaw, Takahiro Seki, Michael Reith, Marta Putrinš, Tanel Tenson, Henrik Strahl, Vasili Hauryliuk, Gemma Catherine Atkinson

    Journal of molecular biology   431 ( 18 ) 3568 - 3590  2019.08  [Refereed]  [International journal]

     View Summary

    Within the larger ABC superfamily of ATPases, ABCF family members eEF3 in Saccharomyces cerevisiae and EttA in Escherichia coli have been found to function as ribosomal translation factors. Several other ABCFs including biochemically characterized VgaA, LsaA and MsrE confer resistance to antibiotics that target the peptidyl transferase center and exit tunnel of the ribosome. However, the diversity of ABCF subfamilies, the relationships among subfamilies and the evolution of antibiotic resistance (ARE) factors from other ABCFs have not been explored. To address this, we analyzed the presence of ABCFs and their domain architectures in 4505 genomes across the tree of life. We find 45 distinct subfamilies of ABCFs that are widespread across bacterial and eukaryotic phyla, suggesting that they were present in the last common ancestor of both. Surprisingly, currently known ARE ABCFs are not confined to a distinct lineage of the ABCF family tree, suggesting that ARE can readily evolve from other ABCF functions. Our data suggest that there are a number of previously unidentified ARE ABCFs in antibiotic producers and important human pathogens. We also find that ATPase-deficient mutants of all four E. coli ABCFs (EttA, YbiT, YheS and Uup) inhibit protein synthesis, indicative of their ribosomal function, and demonstrate a genetic interaction of ABCFs Uup and YheS with translational GTPase BipA involved in assembly of the 50S ribosome subunit. Finally, we show that the ribosome-binding resistance factor VmlR from Bacillus subtilis is localized to the cytoplasm, ruling out a role in antibiotic efflux.

    DOI PubMed

    Scopus

    70
    Citation
    (Scopus)
  • Activation of extracytoplasmic function sigma factors upon removal of glucolipids and reduction of phosphatidylglycerol content in Bacillus subtilis cells lacking lipoteichoic acid.

    Takahiro Seki, Takuya Furumi, Michihiro Hashimoto, Hiroshi Hara, Satoshi Matsuoka

    Genes & genetic systems   94 ( 2 ) 71 - 80  2019.04  [Refereed]  [Domestic journal]

     View Summary

    In Bacillus subtilis, extracytoplasmic function (ECF) sigma factors are activated by reduction of phosphatidylglycerol (PG) content, absence of glucolipids, or absence of lipoteichoic acid (LTA). LTA is synthesized by polymerization of the glycerophosphate moiety of PG onto diglucosyldiacylglycerol (DGlcDG), a major glucolipid in B. subtilis, in the plasma membrane. Thus, reduction of PG content or absence of glucolipids might cause some changes in LTA, and hence we investigated whether reduction of PG content or absence of glucolipids induces the activation of ECF sigma factors independently from an ensuing change in LTA. Disruption of ugtP, responsible for glucolipid synthesis, in cells lacking LTA caused an additive increase of activation levels of σM, σX, σV and σY (3.1-, 2.2-, 2.1- and 1.4-fold, respectively), relative to their activation levels in cells lacking LTA alone. Reduction of PG content (by repressing Pspac-pgsA) in the cells lacking LTA caused an additive increase of activation levels of σM, σW and σV (2.3-, 1.9- and 2.2-fold, respectively). These results suggested that absence of glucolipids or reduction of PG alone, not the possible secondary alteration in LTA, leads to changes that affect the regulation systems of some ECF sigma factors in the plasma membrane.

    DOI PubMed

    Scopus

    6
    Citation
    (Scopus)
  • Construction of a Nonnatural C60 Carotenoid Biosynthetic Pathway.

    Ling Li, Maiko Furubayashi, Takuya Hosoi, Takahiro Seki, Yusuke Otani, Shigeko Kawai-Noma, Kyoichi Saito, Daisuke Umeno

    ACS synthetic biology   8 ( 3 ) 511 - 520  2019.03  [Refereed]  [International journal]

     View Summary

    Longer-chain carotenoids have interesting physiological and electronic/photonic properties due to their extensive polyene structures. Establishing nonnatural biosynthetic pathways for longer-chain carotenoids in engineerable microorganisms will provide a platform to diversify and explore the potential of these molecules. We have previously reported the biosynthesis of nonnatural C50 carotenoids by engineering a C30-carotenoid backbone synthase (CrtM) from Staphylococcus aureus. In the present work, we conducted a series of experiments to engineer C60 carotenoid pathways. Stepwise introduction of cavity-expanding mutations together with stabilizing mutations progressively shifted the product size specificity of CrtM toward efficient synthases for C60 carotenoids. By coexpressing these CrtM variants with hexaprenyl diphosphate synthase, we observed that C60-phytoene accumulated together with a small amount of C65-phytoene, which is the largest carotenoid biosynthesized to date. Although these carotenoids failed to serve as a substrate for carotene desaturases, the C25-half of the C55-phytoene was accepted by the variant of phytoene desaturase CrtI, leading to accumulation of the largest carotenoid-based pigments. Continuing effort should further expand the scope of carotenoids, which are promising components for various biological (light-harvesting, antioxidant, and communicating) and nonbiological (photovoltaic, photonic, and field-effect transistor) systems.

    DOI PubMed

    Scopus

    9
    Citation
    (Scopus)
  • Activation without Proteolysis of Anti-σ Factor RsiV of the Extracytoplasmic Function σ Factor σV in a Glucolipid-Deficient Mutant of Bacillus subtilis

    Takahiro Seki, Kouji Matsumoto, Satoshi Matsuoka, Hiroshi Hara

    Advances in Microbiology   07 ( 04 ) 315 - 327  2017  [Refereed]

    Authorship:Lead author

    DOI

  • Suppression of abnormal morphology and extracytoplasmic function sigma activity in Bacillus subtilis ugtP mutant cells by expression of heterologous glucolipid synthases from Acholeplasma laidlawii.

    Satoshi Matsuoka, Takahiro Seki, Kouji Matsumoto, Hiroshi Hara

    Bioscience, biotechnology, and biochemistry   80 ( 12 ) 2325 - 2333  2016.12  [Refereed]  [International journal]

     View Summary

    Glucolipids in Bacillus subtilis are synthesized by UgtP processively transferring glucose from UDP-glucose to diacylglycerol. Here we conclude that the abnormal morphology of a ugtP mutant is caused by lack of glucolipids, since the same morphology arises after abolition of glucolipid production by disruption of pgcA and gtaB, which are involved in UDP-glucose synthesis. Conversely, expression of a monoglucosyldiacylglycerol (MGlcDG) produced by 1,2-diacylglycerol 3-glucosyltransferase from Acholeplasma laidlawii (alMGS) almost completely suppressed the ugtP disruptant phenotype. Activation of extracytoplasmic function (ECF) sigmas (SigM, SigV, and SigX) in the ugtP mutant was decreased by alMGS expression, and was suppressed to low levels by MgSO4 addition. When alMGS and alDGS (A. laidlawii 1,2-diacylglycerol-3-glucose (1-2)-glucosyltransferase producing diglucosyldiacylglycerol (DGlcDG)) were simultaneously expressed, SigX activation was repressed to wild type level. These observations suggest that MGlcDG molecules are required for maintenance of B. subtilis cell shape and regulation of ECF sigmas, and DGlcDG regulates SigX activity.

    PubMed

  • Repression of the activities of two extracytoplasmic function σ factors, σM and σV, of Bacillus subtilis by glucolipids in Escherichia coli cells.

    Takahiro Seki, Ryota Mineshima, Michihiro Hashimoto, Kouji Matsumoto, Hiroshi Hara, Satoshi Matsuoka

    Genes & genetic systems   90 ( 2 ) 109 - 14  2015  [Refereed]  [Domestic journal]

     View Summary

    Extracytoplasmic function (ECF) σ factors respond to environmental stresses and regulate numerous genes required for adaptation. Under normal growth conditions, the ECF σ factors are sequestered by transmembrane anti-σ factor proteins, from which they are released under stress conditions. In Bacillus subtilis ugtP null mutant cells, which lack glucolipids, three of the seven ECF σ factors, σM, σV and σX, are activated. The Escherichia coli cell membrane does not contain glucolipids. When the genes for these three ECF σ and anti-σ factors were introduced into E. coli cells, expression of lacZ fused to the ECF σ factor-regulated promoters indicated ECF σ factor activity. Additional expression of the ugtP gene in these E. coli cells led to the synthesis of small amounts of glucolipids, and the activities of σM and σV were repressed, but the activity of σX was unaffected. It is likely that glucolipids directly influence anti-σM and anti-σV factors by stabilizing conformations that sequester the respective ECF σ factors.

    DOI PubMed

    Scopus

    7
    Citation
    (Scopus)
  • Induction of extracytoplasmic function sigma factors in Bacillus subtilis cells with defects in lipoteichoic acid synthesis.

    Michihiro Hashimoto, Takahiro Seki, Satoshi Matsuoka, Hiroshi Hara, Kei Asai, Yoshito Sadaie, Kouji Matsumoto

    Microbiology (Reading, England)   159 ( Pt 1 ) 23 - 35  2013.01  [Refereed]  [International journal]

     View Summary

    Lipoteichoic acid (LTA) is an important cell envelope component of Gram-positive bacteria. Bacillus subtilis has four homologous genes for LTA synthesis: ltaS (yflE), yfnI, yqgS and yvgJ. The products LtaS (YflE), YfnI and YqgS are bona fide LTA synthetases, whereas YvgJ functions only as an LTA primase. To clarify whether defects in LTA on the cell envelope trigger extracytoplasmic function (ECF) sigma factors, mRNA levels of the autoregulated ECF sigma factors in cells with singly and multiply deleted alleles of the ltaS homologues were examined by real-time RT-PCR. This revealed that sigM and sigX were induced in cells with a null allele of ΔltaS and ΔyfnI, respectively, and that no ECF sigma factor was induced in cells with a single null allele of ΔyqgS or ΔyvgJ. In cells with double null alleles (ΔltaS and ΔyfnI), sigW and ylaC were induced in addition to sigM and sigX. Cells with triple null alleles (ΔltaS ΔyfnI and ΔyqgS) showed a pattern of induction similar to that of the double null. In cells with quadruple null alleles, sigV and sigY were newly induced. Cells with ΔltaS had approximately 1/4 the diglucosyldiacylglycerol and over 10 times the CDP-diacylglycerol of wild-type cells. Compensatory elevation of the mRNA level of other homologues was observed (in ΔltaS cells the level of yfnI was elevated; in ΔyfnI cells that of yqgS and yvgJ was elevated; both were even higher in ΔltaS ΔyfnI cells). In ΔltaS cells, the mRNA level of yfnI was corroborated to be regulated by σ(M), which is activated in the null mutant cells. In ΔyfnI cells, the mRNA levels of yqgS and yvgJ reverted to less than those of wild-type when a defective sigX allele was introduced. Since sigX was activated in cells with ΔyfnI, this suggests that the induction of yqgS and yvgJ is dependent on σ(X). The LTAs produced by the four ltaS homologues seem to play distinct physiological roles to maintain the full function of LTA on the B. subtilis cell envelope.

    DOI PubMed

    Scopus

    25
    Citation
    (Scopus)

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Research Projects

  • バクテリア細胞膜での膜タンパク質の配向制御ルールの解明と応用

    日本学術振興会  科学研究費助成事業

    Project Year :

    2024.04
    -
    2026.03
     

    関 貴洋

  • 診断酵素の実用新規進化デザインプラットフォーム

    日本学術振興会  科学研究費助成事業

    Project Year :

    2022.08
    -
    2024.03
     

    関 貴洋

  • 難発現・難選抜産業酵素の進化工学プラットフォーム

    国立研究開発法人 新エネルギー・産業技術総合開発機構(NEDO)  官民による若手研究者発掘支援事業 マッチングサポートフェーズ

    Project Year :

    2022.09
    -
    2023.09
     

    関 貴洋

  • Elucidation of glucolipids localization and their chaperone function in Bacillus subtilis

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (B)

    Project Year :

    2015.04
    -
    2019.03
     

    Matsuoka Satoshi, HARA Hiroshi, MATSUMOTO Kouji, SEKI Takahiro

     View Summary

    In Bacillus subtilis, the ugtP mutant, which lacks glyceroglucolipids, shows abnormal morphology and activation of some extracytoplasmic function (ECF) sigma factors (σM, σV and σX) in the log phase. Conversely, the expression of monoglucosyldiacylglycerol (MGlcDG) synthase (alMGS) from Acholeplasma laidlawii almost completely suppresses the ugtP disruptant phenotype. Activation of ECF sigmas in the ugtP mutant is decreased by alMGS expression. When alMGS and alDGS (A. laidlawii diglucosyldiacylglycerol (DGlcDG) synthase) are simultaneously expressed, σX activation is repressed to wild type level. These observations suggest that MGlcDG molecules are required for maintenance of B. subtilis cell shape and regulation of ECF sigmas, and that DGlcDG regulates σX activity. The activation of ECF sigmas is not accompanied by proteolysis of anti-σ. Thus, glyceroglucolipids may have the specific role of helping membrane proteins function by acting in the manner of chaperones.

  • 枯草菌細胞膜糖脂質の環境ストレス応答における役割の解明

    日本学術振興会  科学研究費助成事業 特別研究員奨励費

    Project Year :

    2016.04
    -
    2018.03
     

    関 貴洋

     View Summary

    枯草菌はその細胞膜に糖転移酵素UgtPによって合成される3種類の糖脂質を持っている。ugtP遺伝子を破壊し糖脂質を欠損させた細胞では細胞外ストレス応答因子であるExtraCytoplasimic Function (ECF)シグマ因子(SigM, SigV, SigX)が恒常的に活性化している。ECFシグマ因子は普段, 膜タンパク質であるアンチシグマによって捕縛され活性が抑制されている。
    SigVは細胞壁分解酵素であるリゾチームに応答し, その活性化機構はSigVの特異的アンチシグマRsiVがRIP経路と呼ばれる多段階のプロテアーゼカスケードによって分解されるというものである。しかしRIPプロテアーゼの1つであるRasPを欠損していても, SigVは糖脂質欠損に応答し活性化した。また, 糖脂質欠損株ではRsiVレベルに変化はなく分解は起きていなかった。一方で, あらかじめRsiVを欠損させておくとSigV活性に糖脂質欠損の影響は見られなくなった。これらの結果は, 糖脂質欠損によるSigVの活性化機構はRIP経路を介したRsiVの分解とは異なる機構によることを示している。
    さらに, RsiVの細胞外ドメインを糖脂質欠損には応答しないRsiWの細胞外ドメインと交換したキメラタンパク質は糖脂質欠損に応答しなかった。また, RsiV の66番目のアラニンをトリプトファンに置換した変異RsiVも糖脂質欠損には応答しなかった。これらの結果より, 糖脂質欠損によるSigVの活性化機構は, RsiVの細胞ドメインから始まる立体構造変化であることが示唆された。

  • Structure and function of bacterial lipid domains

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C)

    Project Year :

    2012.04
    -
    2016.03
     

    MATSUMOTO Kouji, HARA Hiroshi, MATSUOKA Satoshi, SADAIE Yoshito, HASHIMOTO Michihiro, KUSAKA Jin, SHUTO Satoshi, ISHIKAWA Kazuki, IMAI Yukiko, TANIGUCHUI Aya, ITOU Aya, MIYAGAWA Hiroyoshi, UMEKAWA Mitsuru, KONDO Daitetsu, SEYA Manato, MINESHIMA Ryota, MIYAMATSU Saori, MATSUSHIMA Wakana, SEKI Takahiro, NISHINO Yuki, FURUKAWA Yugo, SAITO Tomo, NATORI Kohei

     View Summary

    To clarify the structure and function of bacterial lipid domains, we have adopted following two approaches. i) To elucidate the mechanism of formation of cardiolipin domain in Bacillus subtilis cells, the function of C-terminal α-helices of cardiolipin synthase is examined for septal membrane localization by fluorescence microscopy and Western blotting using GFP-ClsA fusion proteins. The enzyme is shown to be septally localized by means of its C-terminal α-helices, indicating that the C-terminal α-helices of the enzyme have a function of membrane targeting. ii) B. subtilis MinD is examined for septal localization in minJ mutant cells and is shown to be septally localized by means of the membrane targeting sequence at its C-terminus. This indicates that a correction in the current model of the sequential interaction for MinD binding to septal membranes is required.

  • Structure and formation of bacterial lipid domains

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C)

    Project Year :

    2009
    -
    2011
     

    MATSUMOTO Kouji, HARA Hiroshi, MATSUOKA Satoshi

     View Summary

    Cardiolipin and phosphatidylethanolamine are localized in the septal and polar membranes, not distributed homogeneously, in Bacillus subtilis cells. In order to clarify the structure and mechanism of formation of bacterial lipid domains, we have adopted following two approaches. (i) To examine the distribution of other membrane lipids, we have screened a library of oligopeptides with random amino acid sequence to develop new probes for specific detection of the other lipids. (ii) To study the mechanism of lipid domain formation, the means to localize septally of lipid synthases and MinD, which regulates the position of cell division, is examined with special focus on the region at its COOH-terminus.

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Misc

  • ミニカロテノイド生合成経路の実験室内進化

    荒木優衣, 尾島匠, 関貴洋, 梅野太輔

    日本遺伝学会大会プログラム・予稿集   95th (CD-ROM)  2023

    J-GLOBAL

  • スクアレン合成酵素のカロテノイド合成酵素としてのサイズ進化

    安藤大翔, 尾島匠, 関貴洋, 梅野太輔

    日本遺伝学会大会プログラム・予稿集   95th (CD-ROM)  2023

    J-GLOBAL

  • 金属結合モチーフのハイスループット解析・進化プラットフォーム

    田中琴葉, 関貴洋, 梅野太輔

    日本遺伝学会大会プログラム・予稿集   95th (CD-ROM)  2023

    J-GLOBAL

  • 膜貫通型シグナル伝達系のゼロベース設計

    関貴洋, 田中琴葉, 矢内祐希, 梅野太輔, 梅野太輔

    日本遺伝学会大会プログラム・予稿集   95th (CD-ROM)  2023

    J-GLOBAL

  • Periplasm Display System for Screening of Novel Enzyme Properties

    関貴洋, 田中琴葉, 木村友紀, 梅野太輔, 梅野太輔

    日本生物工学会大会講演要旨集   75th  2023

    J-GLOBAL

  • Lanthanide sensors using periplasmic display technology

    田中琴葉, 関貴洋, 梅野太輔

    日本生物工学会大会講演要旨集   75th  2023

    J-GLOBAL

  • Laboratory evolution of biosynthetic routes for ”ex-natural” terpenoids

    梅野太輔, 尾島匠, 関貴洋, 大谷悠介, 河合繁子

    日本農芸化学会大会講演要旨集(Web)   2022  2022

    J-GLOBAL

  • 低分子結合による融合パートナーの安定性変化がもたらす酵素進化能への影響

    塚田美結, 関貴洋, 木村友紀, 河合(野間)繁子, 梅野太輔, 梅野太輔

    日本遺伝学会大会プログラム・予稿集   94th (CD-ROM)  2022

    J-GLOBAL

  • 酵素の金属補酵素選択性の実験室内進化

    関貴洋, 梅野太輔, 梅野太輔

    日本遺伝学会大会プログラム・予稿集   94th (CD-ROM)  2022

    J-GLOBAL

  • Evolutionary design of non-allosteric biosensors

    梅野太輔, 木村友紀, 関貴洋

    日本生物工学会大会講演要旨集   74th  2022

    J-GLOBAL

  • Systematic analysis of the interaction of microbial rhodopsins with membrane lipids.

    関貴洋, 斉藤遥平, 須藤雄気, 村田武士, 河合(野間)繁子, 梅野太輔

    日本農芸化学会大会講演要旨集(Web)   2020  2020

    J-GLOBAL

  • 【NEDOスマートセルプロジェクト】メタボライトセンサ構築技術 スマートセル開発のためのメタボライトセンサ製作技術

    関 貴洋, 小林 一幾, 梅野 太輔

    バイオサイエンスとインダストリー   77 ( 6 ) 516 - 517  2019.11

    J-GLOBAL

  • 【天然物化学研究の新展開】二次代謝経路の一次代謝化技術 融和的入植と高出力化のための生合成リデザイン学

    大谷 悠介, 関 貴洋, 梅野 太輔

    ファルマシア   55 ( 7 ) 658 - 661  2019.07

     View Summary

    二次代謝経路(天然物経路)は生理活性と新規酵素の宝庫であり,リデザインも容易である。一方で,これを一次代謝に匹敵する馬力で高度に運転するためには,多くの新しい工学的努力を要する。本稿では,筆者たちのテルペノイド合成経路の進化工学の経験をもとに,天然物生合成経路の高効率運転を目指したリデザイン技術のあり方について議論する。

    DOI CiNii

  • 二次代謝経路の一次代謝化技術 融和的入植と高出力化のための生合成リデザイン学

    大谷悠介, 関貴洋, 梅野太輔

    ファルマシア(Web)   55 ( 7 )  2019

    J-GLOBAL

  • 非対称カロテノイド生合成経路の代謝進化工学

    尾島匠, 関貴洋, LI Ling, 河合繁子, 斎藤恭一, 梅野太輔

    日本農芸化学会大会講演要旨集(Web)   2019  2019

    J-GLOBAL

  • 枯草菌糖脂質合成酵素遺伝子ugtPの発現制御解析

    松岡聡, 竹本愛奈, 関貴洋, 松本幸次, 朝井計, 原弘志

    日本農芸化学会大会講演要旨集(Web)   2017  2017

    J-GLOBAL

  • 糖脂質欠損による枯草菌ECFシグマ因子σvの活性化機構の解析

    関貴洋, 松岡聡, 松本幸次, 原弘志

    脂質生化学研究   58  2016

    J-GLOBAL

  • 糖脂質の欠損による枯草菌ECFシグマ因子σVの活性化メカニズムの解析

    関貴洋, 松岡聡, 松本幸次, 原弘志

    日本農芸化学会大会講演要旨集(Web)   2016  2016

    J-GLOBAL

  • キメラアンチシグマ因子を用いた糖脂質欠損による枯草菌σvの活性化機構の解析

    関貴洋, 松岡聡, 松本幸次, 原弘志

    日本遺伝学会大会プログラム・予稿集   88th  2016

    J-GLOBAL

  • 枯草菌糖脂質合成酵素遺伝子ugtP欠損株におけるECFシグマ因子の活性化機構の解析

    関貴洋, 峯島良太, 松岡聡, 松本幸次, 原弘志

    脂質生化学研究   57  2015

    J-GLOBAL

  • 枯草菌糖脂質欠損株におけるECFシグマ因子σvの活性化機構の解析

    関貴洋, 松岡聡, 松本幸次, 原弘志

    日本遺伝学会大会プログラム・予稿集   87th  2015

    J-GLOBAL

  • 枯草菌SigIの制御における糖脂質の影響

    松岡聡, 関貴洋, 野辺加織, 松本幸次, 原弘志

    日本農芸化学会関東支部講演要旨集   2014 ( Oct )  2014

    J-GLOBAL

  • 枯草菌ECFシグマ因子の活性制御における糖脂質の役割

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