Akio Kanai

Akio Kanai

Faculty of Environment and Information Studies
Graduate School of Media and Governance
DegreesPh. D. (University of Tokyo)
Short BiographyDr. Akio Kanai was born in Tokyo, Japan. He graduated from Waseda University in 1985, and obtained a PhD in Molecular Biology by thesis for research done at the University of Tokyo in 1990. After finishing a postdoctoral training at National Institute of Health, USA (1990-1992), 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 became Professor in April, 2006. His major research fields include molecular cellular biology and gene regulation using a variety of organisms. His work in life sciences has led him to his present research of analyzing RNA-binding proteins and non-coding RNAs.

Research Activities & Projects:
(1) RNA-binding proteins & RNA-related enzymes
(2) Non-coding RNAs (microRNA & small RNA)
(3) tRNA & rRNA
(4) Post-transcriptional RNA processing
(5) Developmental regulation of gene expression
(6) Artificial small RNA
(7) Molecular evolution
Areas of ExpertiseMolecular Biology, Molecular Evolution, Developmental Biology
AffiliationsRNA Society, American Association for the Advancement of Science (AAAS), American Society for Microbiology (ASM), Molecular Biology Society of Japan (MBSJ), Japanese Biochemical Society (JBS), RNA Society of Japan, Society of Evolutionary Studies Japan (SJSE).
Selected PublicationsRecent Publications:

○ 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. (2020) Behavioral and brain- transcriptomic synchronization between the two opponents of a fighting pair of the fish Betta splendens. PLOS Genetics https://doi.org/10.1371/journal.pgen.1008831

○ Hayashi, Y., Mori, M., Igarashi, K., Tanaka, K., Takehara, A., Ito-Matsuoka, Y., Kanai, A., Yaegasgi, N., Soga, T. and Matsui, Y. (2020) Proteomic and metabolomic analyses uncover sex-specific regulatory pathways in mouse fetal germline differentiation. Biology of Reproduction in press.

○ Saito, M., Sato, A., Nagata, S., Tamaki, S., Tomita, M., Suzuki, H., and Kanai, A. (2019) Large-scale Molecular Evolutionary Analysis Uncovers a Variety of Polynucleotide Kinase Clp1 Family Proteins in the Three Domains of Life. Genome Biology and Evolution 11(10): 2713-2726.

○ Kanai, A. and Yoshihisa, T. (2019) Editorial: Current Advances in the Research of RNA Regulatory Enzymes. Frontiers in Genetics 10: 973.

○ Tamaki, S., Tomita, M., Suzuki, H. and Kanai, A. (2018) Systematic analysis of the binding surfaces between tRNAs and their respective aminoacyl tRNA synthetase based on structural and evolutionary data. Frontiers in Genetics 8: 227.

○ Nagata, S., Imai, J., Makino, G., Tomita, M. and Kanai, A. (2017) Evolutionary analysis of HIV-1 Pol proteins reveals representative residues for viral subtype differentiation. Frontiers in Microbiology 8: 2151.

○ Noro, E., Mori, M., Makino, G., Takai, Y., Ohnuma, S., Sato, A., Tomita, M., Nakahigashi, K. and Kanai, A. (2017) Systematic characterization of artificial small RNA-mediated inhibition of Escherichia coli growth. RNA Biology 14(2): 206-218.

○ Hayashi, Y., Otsuka, K., Ebina, M., Igarashi, K., Takehara, A., Matsumoto, M., Kanai, A., Igarashi, K., Soga, T. and Matsui, Y. (2017) Distinct requirements for energy metabolism in mouse primordial germ cells and their reprogramming to embryonic germ cells. Proceedings of the National Academy of Sciences. U. S. A. 114(31): 8289-8294.

○ Ikeda, Y., Okada, Y., Sato, A., Kanai, T., Tomita, M., Atomi, H. and Kanai, A. (2017) An archaeal RNA binding protein, FAU-1, is a novel ribonuclease related to rRNA stability in Pyrococcus and Thermococcus. Scientific Reports 7: 12674.

○ Hamashima, K., Tomita, M. and Kanai, A. (2016) Expansion of non-canonical V-arm-containing tRNAs in eukaryotes. Molecular Biology and Evolution 33(2): 530-540.

○ Yamaguchi, S., Aoki, N., Takehara, A., Mori, M., Kanai, A., Matsushima, T. and Homma, K. J. (2016) Involvement of nucleotide diphosphate kinase 2 in the reopening of the sensitive period of filial imprinting of domestic chicks (Gallus gallus domesticus). Neuroscience Letters 612: 32-37.

○ Ikeda, T. K., Hirose, Y., Hiraoka, K., Noro, E., Fujishima, K., Tomita, M. and Kanai, A. (2015) Identification, expression, and molecular evolution of microRNAs in the “living fossil” Triops cancriformis (tadpole shrimp). RNA 21(2): 230-242.

○ Hamashima, K., Mori, M., Andachi, Y., Tomita, M., Kohara, Y. and Kanai, A. (2015) Analysis of genetic code ambiguity arising from nematode-specific misacylated tRNAs. PLOS ONE 10(1): e0116981.

○ Hirose, Y., Ikeda, T. K., Noro, E., Hiraoka, K., Tomita, M. and Kanai, A. (2015) Precise mapping and dynamics of tRNA-derived fragments (tRFs) in the development of Triops cancriformis (tadpole shrimp). BMC Genetics 16: 83.

○ Kanai, A. (2015) Disrupted tRNA genes and tRNA fragments: a perspective on tRNA gene evolution. Life (Basel) 5(1): 321-331. Review

○ Fujishima, K. and Kanai, A. (2014) tRNA gene diversity in the three domains of life. Frontiers in Genetics 5: 142. Review

○ Kanai, A. (2014) Welcome to the new tRNA world! Frontiers in Genetics 5: 336. Editorial Article


○ Nakahigashi, K., Takai, Y., Shiwa, Y., Wada, M., Honma, M., Yoshikawa, H., Tomita, M., Kanai, A. and Mori. H. (2014) Effect of codon adaptation on codon-level and gene-level translation efficiency in vivo. BMC Genomics 15(1): 1115.

○ Matsui, M., Tomita, M. and Kanai, A. (2013) Comprehensive computational analysis of bacterial CRP/FNR superfamily and its target motifs reveals stepwise evolution of transcriptional networks. Genome Biology and Evolution 5(2): 267-282.

○ Hamashima, K. and Kanai, A. (2013) Alternative genetic code for amino acids and transfer RNA revisited. Biomolecular Concepts 4(3): 309-318. Review

○ Kanai, A. (2013) Molecular evolution of disrupted transfer RNA genes and their introns in archaea. in “Evolutionary Biology: Exobiology and Evolutionary Mechanisms” Springer-Verlag Berlin Heidelberg, Germany. pp. 181-193. Review

○ Fujishima, K. and Kanai, A. (2013) Split Genes in “Brenner’s Encyclopedia of Genetics” 2nd edition, Elsevier Academic Press, USA. pp. 543-544.

○ Soma, A., Sugahara, J., Onodera, A., Yachie, N., Kanai, A., Watanabe, S., Yoshikawa, H., Ohnuma, M., Kuroiwa, H., Kuroiwa, T. and Sekine, Y. (2013) Identification of highly-disrupted tRNA genes in nuclear genome of the red alga, Cyanidioschyzon merolae 10D. Scientific Reports 3: 2321.

○ Hamashima, K., Fujishima, K., Masuda, T., Sugahara, J., Tomita, M. and Kanai, A. (2012) Nematode-specific tRNAs that decode an alternative genetic code for leucine. Nucleic Acids Research 40(8): 3653-3662.

○ Murakami, S., Fujishima, K., Tomita, M. and Kanai, A. (2012) Metatranscriptomic analysis of microbes in an ocean-front deep subsurface hot spring reveals novel small RNAs and type-specific tRNA degradation. Applied and Environmental Microbiology 78(4): 1015-1022.

○ Sugahara, J., Fujishima, K., Nunoura, T., Takaki, Y., Takami, H., Takai, K., Tomita, M. and Kanai, A. (2012) Genomic heterogeneity in a natural archaeal population suggests a model of tRNA gene disruption. PLoS ONE 7(3): e32504.

○ Hirata, A., Fujishima, K., Yamagami, R., Kawamura, T., Banfield, JF., Kanai, A. and Hori, H. (2012) X-ray structure of the fourth type of archaeal tRNA splicing endonuclease: Insights into the evolution of a novel three-unit composition and a unique loop involved in broad substrate specificity. Nucleic Acids Research 40(20): 10554-10566.

○ Fujishima, K., Sugahara, J., Miller, CS., Baker BJ., Di Giulio, M., Takesue, K., Sato, A., Tomita, M., Banfield, JF. and Kanai, A. (2011) A novel three-unit tRNA splicing endonuclease found in ultrasmall archaea possesses broad substrate specificity. Nucleic Acids Research 39(22): 9695-9704.

○ Sato, A., Soga, T., Igarashi, K., Takesue, K., Tomita, M. and Kanai, A. (2011) GTP-dependent RNA 3'-terminal phosphate cyclase from the hyperthermophilic archaeon Pyrococcus furiosus. Genes to Cells 16: 1190-1199.

○ Shinhara, A., Matsui, M., Hiraoka, K., Nomura, W., Hirano, R., Nakahigashi, K., Tomita, M., Mori, H. and Kanai, A. (2011) Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli. BMC Genomics 12: 428.

○ Komasa, M., Fujishima, K., Hiraoka, K., Shinhara, A., Lee, B.-S., Tomita, M. and Kanai, A. (2011) A screening system for artificial small RNAs that inhibit the growth of Escherichia coli. The Journal of Biochemistry 150(3): 289-294.

○ Nunoura, T., Takaki, Y., Kakuta, J., Nishi, S., Sugahara, J., Kazama, H., Chee, G.-J., Hattori, M., Kanai, A., Atomi, H., Takai, K. and Takami, H. (2011) Insights into the evolution of archaea and eukaryotic protein modifier systems reveled by the genome of a novel archaeal group. Nucleic Acids Research 39 (8): 3204-3223.

○ Abe, T., Ikemura, T., Sugahara, J., Kanai, A., Ohara, Y., Uehara, H., Kinouchi, M., Kanaya, S., Yamada, Y., Muto, A. and Inokuchi, H. (2011) tRNADB-CE 2011: tRNA gene database curated manually by experts. Nucleic Acids Research 39: D210-D213.

○ Saito, R., Kohno, K., Okada, Y., Osada, Y., Numata, K., Kohama, C., Watanabe, K., Nakaoka, H., Yamamoto, N., Kanai, A., Yasue, H., Murata, S., Abe, K., Tomita, M., Ohkohchi, N. and Kiyosawa, H. (2011) Comprehensive expressional analyses of antisense transcripts in colon cancer tissues using artificial antisense probes. BMC Medical Genomics 4: 42.

○ Watanabe, Y. and Kanai, A. (2011) Systems biology reveals microRNA-mediated gene regulation. Frontiers in Genetics 2: 29. Review

○ Takane, K. and Kanai, A. (2011) Vertebrate-virus-encoded microRNAs and their sequence conservation. Japanese Journal of Infectious Diseases 64(5): 357-366. Invited Review

○ Fujishima, K. and Kanai, A. (2011) Diversity, function and processing of archaeal non-coding RNAs. in “Archaea: Structure, Habitats and Ecological Significance” Nova Science Publishers, Inc. New York. pp. 69-94. Review

Selected Previous Papers:

○ Fujishima, K., Sugahara, J., Tomita, M. and Kanai, A. (2010) Large-scale tRNA intron transposition in the archaeal order Thermoproteales represents a novel mechanism of intron gain. Molecular Biology and Evolution 27(10): 2233-2243.

○ Takane, K., Fujishima, K., Watanabe, Y., Sato, A., Saito, N., Tomita, M. and Kanai, A. (2010) Computational prediction and experimental validation of evolutionarily conserved microRNA target genes in bilaterian animals. BMC Genomics 11: 101.

○ Kitamura, S., Fujishima, K., Sato, A., Tsuchiya, D., Tomita, M. and Kanai, A. (2010) Characterization of RNase HII substrate recognition using RNase HII-Argonaute chimeric enzymes from Pyrococcus furiosus. Biochemical Journal 426: 337-344.

○ Kanai, A., Sato, A., Fukuda, Y. Okada, K., Matsuda, T., Sakamoto, T., Muto, Y., Yokoyama, S., Kawai, G. and Tomita, M. (2009) Characterization of a heat-stable enzyme possessing GTP-dependent RNA ligase activity from a hyperthermophilic archaeon, Pyrococcus furiosus. RNA 15(3): 420-431.

○ Fujishima, K., Sugahara, J., Kikuta, K., Hirano, R., Sato, A., Tomita, M. and Kanai, A. (2009) Tri-split tRNA is a transfer RNA made from 3 transcripts that provides insight into the evolution of fragmented tRNAs in archaea. Proceedings of the National Academy of Sciences. U. S. A. 106(8): 2683-2687.

○ Sugahara, J., Kikuta, K., Fujishima, K., Yachie, N., Tomita, M. and Kanai, A. (2008) Comprehensive analysis of archaeal tRNA reveals rapid increase of tRNA introns in the order Thermoproteales. Molecular Biology and Evolution 25(12): 2709-2716.

○ Ishii, N., Nakahigashi, K., Baba, T., Robert, M., Soga, T., Kanai, A., Hirasawa, T., Naba, M., Hirai, K., Hoque, A., Kakazu, Y., Sugawara, K., Igarashi, S., Harada, S., Masuda, T., Sugiyama, N., Togashi, T., Hasegawa, M., Takai, Y., Yugi, K., Arakawa, K., Iwata, N., Toya, Y., Nakayama, Y., Nishioka, T., Shimizu, K., Mori, H. and Tomita, M. (2007) Multiple high throughput analyses monitor the response of E. coli to perturbations. Science 316: 593-597.

○ Fujishima, K., Komasa, M., Kitamura, S., Suzuki, H., Tomita, M. and Kanai, A. (2007) Proteome-wide prediction of novel DNA/RNA-binding proteins using amino acid composition and periodicity in hyperthermophilic archeaon Pyrococcus furiosus. DNA Research 14: 91-102.

○ Kochiwa, H., Tomita, M. and Kanai, A. (2007) Evolution of ribonuclease H genes in prokaryotes to avoid inheritance of redundant genes. BMC Evolutionary Biology 7:128.

○ Watanabe, Y., Tomita, M. and Kanai, A. (2007) Computational method for microRNA target prediction. Methods in Enzymology 427: 65-86. Review

○ Soma, A., Onodera, A., Sugahara, J., Kanai, A., Yachie, N., Tomita, M., Kawamura, F. and Sekine, Y. (2007) A novel processing pathway via a circular RNA intermediate of permutated tRNA genes in Cyanidioschyzon merolae. Science 318: 450-453.

○ Kanai, A., Sato, A., Imoto, J. and Tomita, M. (2006) Archaeal Pyrococcus furiosus thymidylate synthase 1 is an RNA-binding protein. Biochemical Journal 393: 373-379.

○ Numata, K., Kanai, A., Saito, R., Kondo, S., Adachi, J., Wilming, L. G., Hume, D. A., RIKEN GER Group Members, Hayashizaki, Y. and Tomita, M. (2003) Identification of putative non-coding RNAs among the RIKEN mouse full-length cDNA collection. Genome Research 13: 1301-1306.

○ Kanai, A., Oida, H., Matsuura, N. and Doi, H. (2003) Expression cloning and characterization of a novel gene that encodes the RNA-binding protein FAU-1 from Pyrococcus furiosus. Biochemical Journal 372: 253-261.

Extramural Services:
(1) Frontiers in Genetics (RNA), Associate Editor


(2) Frontiers in Microbiology (Virology), Review Editor

(3) PLOS ONE, Academic Editor
Home Pagehttp://k-ris.keio.ac.jp/Profiles/70/0006999/profile.html
Contact InformationIAB, Keio University, 403-1 Nipponkoku, Daihoji, Tsuruoka, Yamagata 997-0017 Japan TTCK
akio [ at ] sfc.keio.ac.jp
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