FURUKAWA, Ryutaro

写真a

Affiliation

Faculty of Human Sciences, School of Human Sciences

Job title

Assistant Professor(without tenure)

Education 【 display / non-display

  • 2013.04
    -
    2017.03

    Tokyo University of Pharmacy and Life Sciences  

  • 2011.04
    -
    2013.03

    Tokyo University of Pharmacy and Life Sciences  

  • 2007.04
    -
    2011.03

    Tokyo University of Pharmacy and Life Sciences   School of Life Science  

Degree 【 display / non-display

  • 東京薬科大学   博士(生命科学)

Research Experience 【 display / non-display

  • 2019.04
    -
    Now

    Waseda University   Faculty of Human Sciences

  • 2018.08
    -
    2019.03

    東京大学大学院   工学系研究科   学術支援専門職員

  • 2017.09
    -
    2019.03

    Waseda University   School of Human Sciences

  • 2017.04
    -
    2019.03

    Tokyo University of Pharmacy and Life Sciences   School of Life Science

Professional Memberships 【 display / non-display

  •  
     
     

    THE MOLECULAR BIOLOGY SOCIETY OF JAPAN

  •  
     
     

    SOCIETY OF EVOLUTIONARY STUDIES, JAPAN

 

Research Areas 【 display / non-display

  • Evolutionary biology

Papers 【 display / non-display

  • Evolution of Superoxide Dismutases and Catalases in Cyanobacteria: Occurrence of the Antioxidant Enzyme Genes before the Rise of Atmospheric Oxygen

    Mariko Harada, Ayumi Akiyama, Ryutaro Furukawa, Shin-ichi Yokobori, Eiichi Tajika, Akihiko Yamagishi

    Journal of Molecular Evolution   89 ( 8 ) 527 - 543  2021.10

    DOI

  • Ancestral sequence reconstruction produces thermally stable enzymes with mesophilic enzyme-like catalytic properties.

    Ryutaro Furukawa, Wakako Toma, Koji Yamazaki, Satoshi Akanuma

    Scientific reports   10 ( 1 ) 15493 - 15493  2020.09  [International journal]

     View Summary

    Enzymes have high catalytic efficiency and low environmental impact, and are therefore potentially useful tools for various industrial processes. Crucially, however, natural enzymes do not always have the properties required for specific processes. It may be necessary, therefore, to design, engineer, and evolve enzymes with properties that are not found in natural enzymes. In particular, the creation of enzymes that are thermally stable and catalytically active at low temperature is desirable for processes involving both high and low temperatures. In the current study, we designed two ancestral sequences of 3-isopropylmalate dehydrogenase by an ancestral sequence reconstruction technique based on a phylogenetic analysis of extant homologous amino acid sequences. Genes encoding the designed sequences were artificially synthesized and expressed in Escherichia coli. The reconstructed enzymes were found to be slightly more thermally stable than the extant thermophilic homologue from Thermus thermophilus. Moreover, they had considerably higher low-temperature catalytic activity as compared with the T. thermophilus enzyme. Detailed analyses of their temperature-dependent specific activities and kinetic properties showed that the reconstructed enzymes have catalytic properties similar to those of mesophilic homologues. Collectively, our study demonstrates that ancestral sequence reconstruction can produce a thermally stable enzyme with catalytic properties adapted to low-temperature reactions.

    DOI PubMed

  • Establishment of mesophilic-like catalytic properties in a thermophilic enzyme without affecting its thermal stability

    Satoshi Akanuma, Mizumo Bessho, Hikono Kimura, Ryutaro Furukawa, Shin ichi Yokobori, Akihiko Yamagishi

    Scientific Reports   9 ( 1 ) 9346  2019.12  [Refereed]

     View Summary

    © 2019, The Author(s). Thermophilic enzymes are generally more thermally stable but are less active at moderate temperatures than are their mesophilic counterparts. Thermophilic enzymes with improved low-temperature activity that retain their high stability would serve as useful tools for industrial processes especially when robust biocatalysts are required. Here we show an effective way to explore amino acid substitutions that enhance the low-temperature catalytic activity of a thermophilic enzyme, based on a pairwise sequence comparison of thermophilic/mesophilic enzymes. One or a combination of amino acid(s) in 3-isopropylmalate dehydrogenase from the extreme thermophile Thermus thermophilus was/were substituted by a residue(s) found in the Escherichia coli enzyme at the same position(s). The best mutant, which contained three amino acid substitutions, showed a 17-fold higher specific activity at 25 °C compared to the original wild-type enzyme while retaining high thermal stability. The kinetic and thermodynamic parameters of the mutant showed similar patterns along the reaction coordinate to those of the mesophilic enzyme. We also analyzed the residues at the substitution sites from a structural and phylogenetic point of view.

    DOI PubMed

  • Planktonic adaptive evolution to the sea surface temperature in the Neoproterozoic inferred from ancestral NDK of marine cyanobacteria

    Mariko Harada, Aki Nagano, Sota Yagi, Ryutaro Furukawa, Shin ichi Yokobori, Akihiko Yamagishi

    Earth and Planetary Science Letters   522   98 - 106  2019.09  [Refereed]

     View Summary

    © 2019 Elsevier B.V. The optimum growth temperature of ancestral cyanobacteria inhabiting the sea surface in the Neoproterozoic was estimated based on the thermal stability of experimentally reconstructed ancestral NDK enzymes. Ancestral NDKs of cyanobacteria that diversified ∼1.7, ∼1.0, ∼0.9, ∼0.7, ∼0.6, and ∼0.5 billion years ago were reconstructed and analyzed, and the unfolding midpoint temperatures (Tms) ranged from ∼65 °C to ∼70 °C. Among the host of analyzed NDKs, the ancestors of marine, planktonic α-cyanobacteria diversified ≤ ∼1.0 Ga are highly likely to have inhabited marine environments during the Neoproterozoic, while ancestral cyanobacteria diversified ∼1.7 billion years ago were possibly marine but the habitat is less constrained compared to the others. According to the calibration curves derived from extant organisms, the obtained Tms of α-cyanobacteria diversified ≤ ∼1.0 Ga correspond to the range of optimum growth temperatures of around ∼33–48 °C. The temperature range agrees well with the long-term sea temperature trend during Neoproterozoic suggested by δ18O and δ30Si records from marine cherts. Adaptation to the low temperature during the snowball glaciations in the late Neoproterozoic was not observed, implying that adaptation of optimum growth conditions to the episodic low temperature may not have been necessary. Therefore, ancestral marine plankton must have consistently adapted to the interglacial sea surface temperature in the Neoproterozoic, which was approximately 5–20 °C higher than that is today. They may have survived the glaciations by acquiring cold tolerance and/or by suppressing growth rate.

    DOI

  • Eukaryotes appearing

    Shin Ichi Yokobori, Ryutaro Furukawa

    Astrobiology: From the Origins of Life to the Search for Extraterrestrial Intelligence     105 - 121  2019.01

     View Summary

    © Springer Nature Singapore Pte Ltd. 2019. The appearance of eukaryotic cells was a major step in the evolution of terrestrial life. Recent phylogenetic analyses indicate that the Eukaryotes appeared from the Archaebacteria rather than being a distinct domain from Archaebacteria and Eubacteria. The Asgard archaeal group, which shares genes that are otherwise unique to Eukaryotes, has been suggested to be the closest relative to Eukaryotes. However, eukaryotic genes have also been shown to have originated from diverse groups in the Archaebacteria and Eubacteria. Asgard archaeon-like Archaea (Archaebacteria) may have been the host for endosymbiosis of the mitochondrial ancestor (Alphaproteobacteria) and might have been the ancestor of Eukaryotes; nevertheless, horizontal gene transfer from various lineages of Archaebacteria and Eubacteria also appear to have played an important role in the evolution of Eukaryotes.

    DOI

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Misc 【 display / non-display

  • 祖先アミノアシルtRNA合成酵素の復元

    横堀伸一, 馬場柾, 橋本ちひろ, 古川龍太郎, 松田直樹, 松田直樹, 遠藤有紀, 佐藤陸, 笹本峻弘, 横川隆志, 山岸明彦

    日本生化学会大会(Web)   93rd  2020

    J-GLOBAL

  • 祖先アミノアシルtRNA合成酵素の復元に基づく遺伝暗号の進化の解析

    横堀伸一, 馬場柾, 笹本峻弘, 松田直樹, 橋本ちひろ, 村松あやか, 佐藤陸, 遠藤有紀, 宮下奈津実, 丸山真歩, 横川隆志, 古川龍太郎, 古川龍太郎, 山岸明彦

    日本進化学会大会プログラム・講演要旨集(Web)   21st  2019

    J-GLOBAL

  • 祖先Class IaアミノアシルtRNA合成酵素の基質特異性に基づく初期翻訳系の進化

    古川龍太郎, 馬場柾, 松田直樹, 笹本峻弘, 横川隆志, 横堀伸一, 山岸明彦

    日本分子生物学会年会プログラム・要旨集(Web)   42nd  2019

    J-GLOBAL

  • Class IIaアミノアシルtRNA合成酵素の分子系統解析に基づく初期翻訳系の進化

    古川龍太郎, 横堀伸一, 山岸明彦

    日本分子生物学会年会プログラム・要旨集(Web)   41st  2018

    J-GLOBAL

  • Evolution of antioxidant enzymes in cyanobacteria and its relationships to the rise of atmospheric oxygen

    AKIYAMA Ayumi, HARADA Mariko, FURUKAWA Ryutaro, YOKOBORI Shin‐ichi, TAJIKA Eiichi, YAMAGISHI Akihiko

    日本地球惑星科学連合大会予稿集(Web)   2018   ROMBUNNO.BCG09‐12 (WEB ONLY)  2018

    J-GLOBAL

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Research Projects 【 display / non-display

  • Analysis of amino acid specificity of aminoacyl-tRNA synthetase before last universal common ancestor

    Grant-in-Aid for Early-Career Scientists

    Project Year :

    2020.04
    -
    2022.03
     

  • 祖先アミノアシルtRNA合成酵素の解析に基づくタンパク質合成系の確立過程の解明

    Project Year :

    2019.10
    -
    2020.03
     

    古川龍太郎

    Authorship: Principal investigator

Presentations 【 display / non-display

  • Evolution of early translation system based on molecular phylogenetic analysis of Class IIa aminoacyl tRNA synthetases

    Ryutaro Furukawa

    Presentation date: 2019.03

  • アミノアシルtRNA合成酵素の分子系統解析に基づく古細菌と真核生物の系統的位置の再検討

    古川龍太郎, 横堀伸一, 山岸明彦

    極限環境生物学会第18回年会 

    Presentation date: 2017.11

  • アミノアシルtRNA合成酵素の分子系統樹に基づく生命の初期進化の解析

    古川龍太郎, 横堀伸一, 山岸明彦

    日本Archaea研究会第30回講演会 

    Presentation date: 2017.09

  • アミノアシルtRNA合成酵素の分子系統解析に基づく初期翻訳系の進化

    古川龍太郎, 横堀伸一, 山岸明彦

    日本進化学会第19回大会 

    Presentation date: 2017.08

  • Searching for Ancestors of Eukaryotic Cells Based on Phylogenetic Analyses of Aminoacyl-tRNA Synthetase

    Ryutaro Furukawa, M. Nakagawa, T. Kuroyanagi, S. Yokobori, A. Yamagishi

    Extremophiles2016 

    Presentation date: 2016.09

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Specific Research 【 display / non-display

  • 祖先class IIaアミノアシルtRNA合成酵素のアミノ酸特異性の解析

    2020  

     View Summary

    HisとGlyの分岐点に当たる祖先ARS (AncHG)のアミノ酸配列から基質アミノ酸との結合に重要な部位を選出し、その部位に当たるアミノ酸を現存する好熱菌であるThermus thermophilusが持つHisRSおよびGlyRSに導入することで、祖先ARSのアミノ酸特異性を調べることにした。AncHGの基質アミノ酸との結合に重要な部位を選出し、TTHis、TTGlyに導入したTTHisancHG、TTGlyancHGを設計し、タンパク質の発現を行った。TTHisancHG、TTGlyancHGは発現したが、不溶性であった。このことから、祖先配列推定の方法を見直す必要がある。

  • 祖先アミノアシルtRNA合成酵素の解析に基づくタンパク質合成系の確立過程の解明

    2019  

     View Summary

    本研究では、20種類のアミノ酸に相当するアミノアシルtRNA合成酵素(ARS)が全て揃う以前の初期生命が持っていたと考えられる原始ARSを推定・復元し、アミノ酸特異性を解析することで、アミノ酸種がタンパク質合成システムに取り込まれた順序を推定し、原始タンパク質合成システムがいかにして誕生し、進化したかを明らかにすることを目的とした。7種のARSの複合系統樹を構築し、ARSの分岐順の推定および、祖先配列推定、祖先配列から推定されるアミノ酸特異性の予測をおこなった。その結果、祖先ARSは想定したよりも狭いアミノ酸特異性を持つと予測された。

 

Syllabus 【 display / non-display