Kanai, Akio

写真a

Affiliation

Graduate School of Media and Governance （Shonan Fujisawa）

Position

Professor

Related Websites

External Links
Page Top ▲

Profile 【 Display / hide 】

  • 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.

Page Top ▲

Message from the Faculty Member 【 Display / hide 】

  • We have been carrying out research mainly related to the molecular biology and molecular evolution of RNAs in a manner that combines bioinformatics and experimental biology. One of our representative studies is the systematic discovery of functional RNAs. For example, through the analysis of experimentally collected mouse full-length cDNA clones, we showed for the first time that a large amount of long noncoding RNAs exist in mammals (Genome Research 2003, in collaboration with RIKEN). Subsequently, we have discovered and reported new molecular species of small RNAs in E. coli (BMC Genomics 2011) and microRNAs in the "living fossil" Triops cancriformis (tadpole shrimp) (RNA 2015), at the genome level. We also reported that artificially synthesized small RNAs can inhibit the growth of E. coli (RNA Biology 2017). Furthermore, we systematized the evolution of group II introns in prokaryotes, known as one of the genes that move across the genome (Frontiers in Microbiology 2022). In addition to these findings, we also contributed to the discovery of various disrupted transfer RNA (tRNA) genes and tRNA-like genes since 2006 (Mol. Biol. Evol. 2008; PNAS. 2009; Nucleic Acids Res. 2011; Mol. Biol. Evol. 2016). We have also reported on the characteristics of a group of enzymes involved in the regulation of RNA molecules and their molecular evolution (RNA 2009; Nucleic Acids Res. 2011; Genome Biol. Evol. 2019). More recently, we reported that the ribosomes of tiny bacteria called CPR bacteria are small and discussed their molecular evolution (RNA 2022).

    Education of undergraduate and graduate students:
    The goal of our RNA research group is to create human resources who can think for themselves. This needs to be learned properly during the student years. In extreme terms, it does not matter who you learn the experimental techniques from, as long as you can learn them correctly. What is important is to be able to think properly about what to study, what to do when in trouble, and how to develop. In other words, it is important for you to be able to develop your research without being bound by the themes of your student days.

Page Top ▲

Profile Summary 【 Display / hide 】

  • It has been 60 years since the flow of genetic information (central dogma) from DNA to RNA to protein was proposed. Although this concept remains unchanged as the basic axis, it has been required to be modified with the discovery of reverse transcriptases in the 1970s and RNA enzymes (ribozymes) in the 1980s. Furthermore, with the discovery of so many non-coding RNAs in the 21st century, the function of the RNA molecules themselves in central dogma has become impossible to ignore. This project focuses on functional RNAs, RNA-binding proteins, and RNA-related enzymes involved in gene regulations, and aims to elucidate new regulatory mechanisms mediated by RNAs. Furthermore, based on the findings obtained through these studies, we will discuss the origin of life, evolution, and the basic regulatory mechanisms of genes.

Page Top ▲

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

display all >>

Page Top ▲

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

Page Top ▲

Academic Degrees 【 Display / hide 】

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

    Structural and expression analysis of gene clusters for Sarcotoxin I and II, antibacterial proteins of flesh fly, Sarcophaga peregrina

Page Top ▲
 

Research Areas 【 Display / hide 】

  • Life Science / Molecular biology (RNA molecular biology)

  • Life Science / Genome biology (Gene evolution)

  • Life Science / Evolutionary biology (Molecular evolution)

Page Top ▲

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

Page Top ▲

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

Page Top ▲
 

Books 【 Display / hide 】

display all >>

Page Top ▲

Papers 【 Display / hide 】

  • Identification of attenuators of transcriptional termination: implications for RNA regulation in Escherichia coli.

    Morita, T., Majdalani, N., Miura, M. C., Inose, R., Oshima, T., Tomita, M., Kanai, A., and Gottesman, S.

    mBio （The American Society for Microbiology (ASM))  13 （ 6 ） e0237122 2022.10

    Research paper (scientific journal), Joint Work, Accepted

    　View Summary

    The regulatory function of many bacterial small RNAs (sRNAs) requires the binding of the RNA chaperone Hfq to the 3′ portion of the sRNA intrinsic terminator, and therefore sRNA signaling might be regulated by modulating its terminator. Here, using a multicopy screen developed with the terminator of sRNA SgrS, we identified an sRNA gene (cyaR) and three protein-coding genes (cspD, ygjH, and rof) that attenuate SgrS termination in Escherichia coli. Analyses of CyaR and YgjH, a putative tRNA binding protein, suggested that the CyaR activity was indirect and the effect of YgjH was moderate. Overproduction of the protein attenuators CspD and Rof resulted in more frequent readthrough at terminators of SgrS and two other sRNAs, and regulation by SgrS of target mRNAs was reduced. The effect of Rof, a known inhibitor of Rho, was mimicked by bicyclomycin or by a rho mutant, suggesting an unexpected role for Rho in sRNA termination. CspD, a member of the cold shock protein family, bound both terminated and readthrough transcripts, stabilizing them and attenuating termination. By RNA sequencing analysis of the CspD overexpression strain, we found global effects of CspD on gene expression across some termination sites. We further demonstrated effects of endogenous CspD under slow growth conditions where cspD is highly expressed. These findings provided evidence of changes in the efficiency of intrinsic termination, confirming this as an additional layer of the regulation of sRNA signaling.

  • 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,  ISSN  13558382

    　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.

display all >>

Page Top ▲

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

display all >>

Page Top ▲

Reviews, Commentaries, etc. 【 Display / hide 】

display all >>

Page Top ▲

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

Page Top ▲

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

    　View Description

    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

Page Top ▲
 

Courses Taught 【 Display / hide 】

  • SPECIAL RESEARCH PROJECT B

    2023

  • SEMINAR B

    2023

  • MASTER SEMINAR

    2023

  • INDEPENDENT RESEARCH

    2023

  • GRADUATION PROJECT 2

    2023

display all >>

Page Top ▲

Courses Previously Taught 【 Display / hide 】

  • CONCEPTUAL FRAMEWORK (SYSTEMS BIOLOGY)

    Keio University

    2018.04
    -
    2019.03
    , 

    Spring Semester

  • GENOMIC MOLECULAR BIOLOGY 1

    Keio University

    2018.04
    -
    2019.03
    , 

    Spring Semester, Lecture

  • GENOMIC MOLECULAR BIOLOGY 2

    Keio University

    2018.04
    -
    2019.03
    , 

    Autumn Semester

  • 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

display all >>

Page Top ▲
 

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
    -
    Present

display all >>

Page Top ▲

Committee Experiences 【 Display / hide 】

  • 2020.05
    -
    Present

    Visiting professor, Yamaguchi University Graduate School of Medicine

  • 2010.10
    -
    Present

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

  • 2010.08
    -
    2023.04

    PLOS ONE, Editorial Board - Academic Editor

  • 2010.06
    -
    Present

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

Page Top ▲