Kanai, Akio

写真a

Affiliation

Graduate School of Media and Governance (Shonan Fujisawa)

Position

Professor

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External Links

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  • Dr. Akio Kanai was born in Tokyo, Japan. He graduated from Waseda University in 1985, and obtained his PhD in molecular biology at the University of Tokyo in 1990. He finished postdoctoral training at the National Institutes of Health, USA (1990-1992), and he was appointed a researcher in the Tokyo Metropolitan Institute of Medical Science (1992-1996). He was a group leader for the Japan Science and Technology Corporation (JST), ERATO Project Group (1996-2001). He was an Associate Professor at the Institute for Advanced Biosciences, Keio University (2001-2006) and accepted a full professorship in April, 2006. Since 2022, he is also a professor of Systems Biology Program, Graduate School of Media and Governance, Keio University. His major research fields include molecular cellular biology and gene regulation in a variety of organisms. His work in life sciences has led him to his present research into RNA-binding proteins and non-coding RNAs.

Message from the Faculty Member 【 Display / hide

  • 研究紹介:
     我々は、生命情報科学と実験生物学を融合する形で、主にRNAの分子生物学、分子進化学に関連する研究を遂行してきました。代表的な研究としては機能性RNAの系統的な発見になります。例えば、実験的に集められたマウス完全長cDNAクローンの解析から、世界で初めて、哺乳類に長鎖ノンコーディングRNAが多量に存在することを示しました (Genome Research 2003、理化学研究所との共同研究)。その後、大腸菌の低分子RNA (BMC Genomics 2011)や、生きた化石生物と呼ばれるカブトエビからマイクロRNA (RNA 2015)の新しい分子種をゲノムレベルで見出し報告しています。また、人工合成した低分子RNAを用いれば大腸菌の増殖を抑制可能であることを報告しています (RNA Biology 2017)。さらに、ゲノム上を動く遺伝子として知られるグループIIイントロンの原核生物での進化を体系化しました (Frontiers in Microbiology 2022)。これらの新しい機能性RNAの研究と一部並行しながら、2006年から約10年をかけて、様々な形状で分断された転移RNA (tRNA)遺伝子やtRNA様の遺伝子の発見に貢献しました (Mol. Biol. Evol. 2008; PNAS. 2009; Nucleic Acids Res. 2011; Mol. Biol. Evol. 2016)。現在、世界で知られている様々な形状のtRNA遺伝子の約半分は我々が提唱したことになります。また、RNA分子の制御に関わる酵素群の性状やその分子進化についても報告してきました (RNA 2009; Nucleic Acids Res. 2011; Genome Biol. Evol. 2019)。最近では、CPRバクテリアと呼ばれる極小のバクテリアのリボソームが小型であることを報告し、その分子進化を議論しました (RNA 2022)。

    学部や大学院学生の教育について:
     RNA研究プロジェクトが目指すのは考えられる人材の創出です。これを学生時代にきちんと学ぶ必要があります。極端な言い方をすれば、実験技術は、正確に習得出来さえすれば、誰から学んでも問題ではありません。大切なのは、何を研究するのか、困った時にどうするか、どう展開していくのかということをきちんと考えられるようになることです。RNA研究グループ内では、学生の各々のテーマを通して、他のグループの大学院生ならば、私の大学院の授業である「先端分子細胞生物学」の演習を通して、このことに言及したいと思っています。すなわち、学生時代のテーマに縛られずに研究を展開していけるようにすることが重要であると判断しています。

Profile Summary 【 Display / hide

  • 遺伝情報の流れとしてDNA→RNA→蛋白質(セントラルドグマ)が提唱されたのは60年も前のことです。この考え方は基本軸として揺るがないでしょうが、1970-80年代における、逆転写酵素や酵素活性を有したRNA (リボザイム)の発見等で、その修正を要求されてきました。また、21世紀になってから極めて沢山のノンコーディングRNAが発見されたことで、セントラルドグマにおけるRNA分子そのものの働きが無視できない状況になってきました。本プロジェクトでは、遺伝子制御に関わる機能性RNAやRNA結合蛋白質およびRNA関連酵素に焦点をあて、RNAレベルで制御される新しいメカニズムの解明を目的とします。またこの研究を通して、遺伝情報制御および成立過程に関わる分子進化的な考察を行います。さらに、これらの知見を基盤として、生命の起源、進化、遺伝子制御について考察していきます。

Career 【 Display / hide

  • 2022.04
    -
    Present

    Professor, Graduate School of Media and Governance, Keio University, Systems Biology Program

  • 2006.04
    -
    Present

    Professor, Institute for Advanced Biosciences, Keio University

  • 2001.04
    -
    2006.03

    Associate Professor, Institute for Advanced Biosciences, Keio University

  • 1996.04
    -
    2001.03

    Group Leader, ERATO Project, Japan Science and Technology Agency (JST)

  • 1992.11
    -
    1996.03

    Researcher, Tokyo Metropolitan Institute of Medical Science, Japan

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Academic Background 【 Display / hide

  • 1987.04
    -
    1990.03

    The University of Tokyo, Graduate School, Division of Pharmaceutical Scienc, Life Science

    Graduate School, Completed, Doctoral course

  • 1985.04
    -
    1987.03

    Waseda University, Graduate School, Division of Science and Engineering, Physics and Applied Physics

    Graduate School, Completed, Master's course

  • 1981.04
    -
    1985.03

    Waseda University, Faculty of Education, Biology

    University, Graduated

Academic Degrees 【 Display / hide

  • Ph. D., The University of Tokyo, Coursework, 1990.03

    センチニクバエ抗菌蛋白ザルコトキシンIおよびII遺伝子ファミリーの構造と発現の解析

 

Research Areas 【 Display / hide

  • Life Science / Molecular biology (RNA molecular biology)

  • Life Science / Genome biology (Gene evolution)

  • Life Science / Evolutionary biology (Molecular evolution)

Research Keywords 【 Display / hide

  • Archaea, Bacteria, RNA viruses

  • Systems biology, Synthetic biology, Genome biology

  • Non-codingRNA, transfer RNA, ribosomal RNA, RNA-related enzymes

  • RNA processing, pre-tRNA-splicing, RNA ligase, Ribonuclease

  • Genetic code, Molecular evolution

Research Themes 【 Display / hide

  • (1) RNA-Binding Proteins & RNA-Related Enzymes, (2) Non-coding RNAs, (3) Origin of Life, (4) Molecular Evolution, (5) Microbiomes of Extreme Environments, (6) Systems Biology of Gene Regulation, (7) Evolution of RNA viruses, 

    2001
    -
    Present

 

Books 【 Display / hide

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Papers 【 Display / hide

  • Features of smaller ribosomes in Candidate Phyla Radiation (CPR) bacteria revealed with a molecular evolutionary analysis

    Megumi Tsurumaki, Motofumi Saito, Masaru Tomita, and Akio Kanai

    RNA (Cold Spring Harbor Laboratory Press)  28 ( 8 ) 1041 - 1057 2022.06

    Research paper (scientific journal), Joint Work, Last author, Corresponding author, Accepted

     View Summary

    The candidate phyla radiation (CPR) is a large bacterial group consisting mainly of uncultured lineages. They have small cells and small genomes, and they often lack ribosomal proteins uL1, bL9, and/or uL30, which are basically ubiquitous in non-CPR bacteria. Here, we comprehensively analyzed the genomic information on CPR bacteria and identified their unique properties. The distribution of protein lengths in CPR bacteria peaks at around 100-150 amino acids, whereas the position of the peak varies in the range of 100-300 amino acids in free-living non-CPR bacteria, and at around 100-200 amino acids in most symbiotic non-CPR bacteria. These results show that the proteins of CPR bacteria are smaller, on average, than those of free-living non-CPR bacteria, like those of symbiotic non-CPR bacteria. We found that ribosomal proteins bL28, uL29, bL32, and bL33 have been lost in CPR bacteria in a taxonomic lineage-specific manner. Moreover, the sequences of approximately half of all ribosomal proteins of CPR differ, in part, from those of non-CPR bacteria, with missing regions or specifically added regions. We also found that several regions in the 16S, 23S, and 5S rRNAs of CPR bacteria are lacking, which presumably caused the total predicted lengths of the three rRNAs of CPR bacteria to be smaller than those of non-CPR bacteria. The regions missing in the CPR ribosomal proteins and rRNAs are located near the surface of the ribosome, and some are close to one another. These observations suggest that ribosomes are smaller in CPR bacteria than those in free-living non-CPR bacteria, with simplified surface structures.

  • Distinct Expansion of Group II Introns During Evolution of Prokaryotes and Possible Factors Involved in Its Regulation

    Masahiro C. Miura, Shohei Nagata, Satoshi Tamaki, Masaru Tomita, and Akio Kanai

    Frontiers in Microbiology (Frontiers Media SA)  13   849080 2022.02

    Research paper (scientific journal), Last author, Corresponding author, Accepted

     View Summary

    Group II introns (G2Is) are ribozymes that have retroelement characteristics in prokaryotes. Although G2Is are suggested to have been an important evolutionary factor in the prokaryote-to-eukaryote transition, comprehensive analyses of these introns among the tens of thousands of prokaryotic genomes currently available are still limited. Here, we developed a bioinformatic pipeline that systematically collects G2Is and applied it to prokaryotic genomes. We found that in bacteria, 25% (447 of 1,790) of the total representative genomes had an average of 5.3 G2Is, and in archaea, 9% (28 of 296) of the total representative genomes had an average of 3.0 G2Is. The greatest number of G2Is per genome was 101 in Arthrospira platensis (phylum Cyanobacteriota). A comprehensive sequence analysis of the intron-encoded protein (IEP) in each G2I sequence was conducted and resulted in the addition of three new IEP classes (U1–U3) to the previous classification. This analysis suggested that about 30% of all IEPs are non-canonical IEPs. The number of G2Is per genome was defined almost at the phylum level, and at least in the following two phyla, Firmicutes, and Cyanobacteriota, the type of IEP was largely associated as a factor in the G2I increase, i.e., there was an explosive increase in G2Is with bacterial C-type IEPs, mainly in the phylum Firmicutes, and in G2Is with CL-type IEPs, mainly in the phylum Cyanobacteriota. We also systematically analyzed the relationship between genomic signatures and the mechanism of these increases in G2Is. This is the first study to systematically characterize G2Is in the prokaryotic phylogenies.

  • Behavioral and brain- transcriptomic synchronization between the two opponents of a fighting pair of the fish Betta splendens.

    Vu, T.-D., Iwasaki, Y., Shigenobu, S., Maruko, A., Oshima, K., Iioka E., Huang, C.-L., Abe, T., Tamaki, S., Lin, Y.-W., Chen, C.-K., Lu, M.-Y., Hojo, M., Wang, H.-V., Tzeng, S.-F., Huang, H.-J., Kanai, A., Gojobori, T., Chiang, T.-Y., Sun, H. S., Li, W.-H., and Okada, N.

    PLOS Genetics (PLOS)  16 ( 6 )  2020.06

    Research paper (scientific journal), Accepted,  ISSN  15537390

     View Summary

    Conspecific male animals fight for resources such as food and mating opportunities but typically stop fighting after assessing their relative fighting abilities to avoid serious injuries. Physiologically, how the fighting behavior is controlled remains unknown. Using the fighting fish Betta splendens, we studied behavioral and brain-transcriptomic changes during the fight between the two opponents. At the behavioral level, surface-breathing, and biting/striking occurred only during intervals between mouth-locking. Eventually, the behaviors of the two opponents became synchronized, with each pair showing a unique behavioral pattern. At the physiological level, we examined the expression patterns of 23,306 brain transcripts using RNA-sequencing data from brains of fighting pairs after a 20-min (D20) and a 60-min (D60) fight. The two opponents in each D60 fighting pair showed a strong gene expression correlation, whereas those in D20 fighting pairs showed a weak correlation. Moreover, each fighting pair in the D60 group showed pair-specific gene expression patterns in a grade of membership analysis (GoM) and were grouped as a pair in the heatmap clustering. The observed pair-specific individualization in brain-transcriptomic synchronization (PIBS) suggested that this synchronization provides a physiological basis for the behavioral synchronization. An analysis using the synchronized genes in fighting pairs of the D60 group found genes enriched for ion transport, synaptic function, and learning and memory. Brain-transcriptomic synchronization could be a general phenomenon and may provide a new cornerstone with which to investigate coordinating and sustaining social interactions between two interacting partners of vertebrates.

  • Large-scale Molecular Evolutionary Analysis Uncovers a Variety of Polynucleotide Kinase Clp1 Family Proteins in the Three Domains of Life

    Saito, M., Sato, A., Nagata, S., Tamaki, S., Tomita, M., Suzuki, H., and Kanai, A.

    Genome Biology and Evolution (Genome Biology and Evolution)  11 ( 10 ) 2713 - 2726 2019.09

    Research paper (scientific journal), Last author, Corresponding author, Accepted

     View Summary

    © 2019 The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. Clp1, a polyribonucleotide 5′-hydroxyl kinase in eukaryotes, is involved in pretRNA splicing and mRNA 3′-end formation. Enzymes similar in amino acid sequence to Clp1, Nol9, and Grc3, are present in some eukaryotes and are involved in prerRNA processing. However, our knowledge of how these Clp1 family proteins evolved and diversified is limited. We conducted a large-scale molecular evolutionary analysis of the Clp1 family proteins in all living organisms for which protein sequences are available in public databases. The phylogenetic distribution and frequencies of the Clp1 family proteins were investigated in complete genomes of Bacteria, Archaea and Eukarya. In total, 3,557 Clp1 family proteins were detected in the three domains of life, Bacteria, Archaea, and Eukarya. Many were from Archaea and Eukarya, but a few were found in restricted, phylogenetically diverse bacterial species. The domain structures of the Clp1 family proteins also differed among the three domains of life. Although the proteins were, on average, 555 amino acids long (range, 196-2,728), 122 large proteins with >1,000 amino acids were detected in eukaryotes. These novel proteins contain the conserved Clp1 polynucleotide kinase domain and various other functional domains. Of these proteins, >80% were from Fungi or Protostomia. The polyribonucleotide kinase activity of Thermus scotoductus Clp1 (Ts-Clp1) was characterized experimentally. Ts-Clp1 preferentially phosphorylates single-stranded RNA oligonucleotides (Km value for ATP, 2.5 μM), or single-stranded DNA at higher enzyme concentrations. We propose a comprehensive assessment of the diversification of the Clp1 family proteins and the molecular evolution of their functional domains.

  • Systematic characterization of artificial small RNA-mediated inhibition of Escherichia coli growth

    Noro, E., Mori, M., Makino, G., Takai, Y., Ohnuma, S., Sato, A., Tomita, M., Nakahigashi, K. and Kanai, A.

    RNA Biology (Taylor & Francis Group)  14 ( 2 ) 206 - 218 2017

    Research paper (scientific journal), Joint Work, Last author, Corresponding author, Accepted

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Papers, etc., Registered in KOARA 【 Display / hide

Reviews, Commentaries, etc. 【 Display / hide

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Research Projects of Competitive Funds, etc. 【 Display / hide

  • 微生物生態系による原子炉内物体の腐食・変質に関する評価研究

    2019.10
    -
    2020.12

    文部科学省, 英知を結集した原子力科学技術・人材育成事業 国際協力型廃炉研究プログラム(廃炉加速化研究プログラム), Elena Shagimardanova, Research grant, Principal investigator

     View Summary

    高放射能環境でも一部の微生物は繁殖する。また、高放射能に繰り返し曝されることにより、放射能耐性を獲得する。福島第一原子力発電所(1F)事故では、定常的に微生物を含んだ地下水が流れ込んでおり、その内部に微生物群集が形作られている可能性が高い。このことから、1F敷地内外の地下水や放射能汚染水のメタゲノム解析により、それらの微生物群集の実態(生物種の群集構造と発現遺伝子プロファイル)を明らかにする。微生物群集の代謝反応経路を推定することにより、微生物生態系の原子炉内構造物に対する影響を調べ、微生物により燃料デブリや構造材(コンクリート、鉄材など)の腐食・変性が促進される可能性を検討する。それらを基に、微生物群集の制御に関する指針を提案するとともに、定常的な生物環境モニタリングのための拠点形成を進める。

  • 多様性を有するRNAキナーゼの進化情報解析とその情報に基づいた酵素機能の改変

    2017.04
    -
    2020.03

    MEXT,JSPS, Grant-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (C), Principal investigator

  • Identification and biochemical characterization of RNA ligases in archaea

    2010.04
    -
    2012.03

    日本学術振興会, 科研費 , Akio Kanai, 基盤研究(B), Principal investigator

Awards 【 Display / hide

  • 「平成29年度『科研費』審査委員」表彰

    金井昭夫, 2017.09, 独立行政法人 日本学術振興会

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    科学研究費助成事業の審査に関し、有意義な審査意見を付したことによる

 

Courses Taught 【 Display / hide

  • SPECIAL RESEARCH PROJECT B

    2022

  • SEMINAR B

    2022

  • MASTER SEMINAR

    2022

  • INDEPENDENT RESEARCH

    2022

  • GRADUATION PROJECT 2

    2022

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Courses Previously Taught 【 Display / hide

  • GENOMIC MOLECULAR BIOLOGY 1

    Keio University

    2018.04
    -
    2019.03

    Spring Semester, Lecture

  • ADVANCED MOLECULAR AND CELLULAR BIOLOGY

    Keio University

    2018.04
    -
    2019.03

    Autumn Semester

  • ADVANCED RESEARCH (SYSTEMS BIOLOGY)

    Keio University

    2018.04
    -
    2019.03

    Autumn Semester

  • GENOMIC MOLECULAR BIOLOGY 2

    Keio University

    2018.04
    -
    2019.03

    Autumn Semester

  • CONCEPTUAL FRAMEWORK (SYSTEMS BIOLOGY)

    Keio University

    2018.04
    -
    2019.03

    Spring Semester

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Memberships in Academic Societies 【 Display / hide

  • RNA Society, 

    1999
    -
    Present
  • American Association for the Advancement of Science (AAAS), 

    2001
    -
    Present
  • American Society for Microbiology (ASM)

     
  • RNA Society of Japan (2021 Annual Meeting Organizer) , 

    2012.04
    -
    Present
  • Molecular Biology Society of Japan (MBSJ) , 

    1990
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    Present

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Committee Experiences 【 Display / hide

  • 2020.05
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    Present

    Visiting professor, Yamaguchi University Graduate School of Medicine

  • 2010.10
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    Present

    Frontiers in Genetics (RNA), Editorial Board – Associate Editor

  • 2010.08
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    Present

    PLOS ONE, Editorial Board - Academic Editor

  • 2010.06
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    Present

    Frontiers in Microbiology (Virology), Editorial Board - Review Editor