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Field

Molecular and Chemical Life Science :
Chemical Biology

Research

JAPANESE
Assistant Professor YOKOYAMA Takeshi
Campus Katahira campus
Laboratory Applied Biological Molecular Science
Tel +81-22-217-6206
E-mail takeshi.yokoyama.d1＠tohoku.ac.jp
Website http://www.lifesci.tohoku.ac.jp/labmos/index.html
researchmap
https://researchmap.jp/yokotake/?lang=english


Using single particle cryo-electron microscopy, I try to reveal shapes and motion of ribosome complexes, which is the protein synthesis machinery in cells. This is really interesting as if finding small creatures and observing their behavior in nature.
Career
2003 BSc: School of Agriculture, Meiji University.
2005 MSc: Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo.
2008 PhD: Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo.
2008-2012 Wadsworth Center, New York State Department of Health. Creative Biomedical Research Institute. Research Scientist.
2012-2013 Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology. Visiting Scientist.
2013-2018 Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies (CLST). Research Scientist.
2018- RIKEN Center for Biosystems Dynamics Research. Research Scientist.
2019- Graduate School of Life Sciences, Tohoku University. Assistant Professor.
2020- The Advanced Research Center for Innovations in Next-Generation Medicine (INGEM), Tohoku University.
2021- Prominent Research Fellow of Tohoku University.
 
Selected Publications
  1. Mayuki Tanaka#, Takeshi Yokoyama#, Hironori Saito#, Madoka Nishimoto, Kengo Tsuda, Naoyuki Sotta, Hideki Shigematsu, Mikako Shirouzu, Shintaro Iwasaki*, Takuhiro Ito*, and Toru Fujiwara*
    Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1 at the A site. 
    Nature Chemical Biology (2024)
    #equal contribution
     
  2. Junta Tomono#, Kosuke Asano#, Takuma Chiashi, Masato Suzuki, Masayuki Igarashi, Yoshiaki Takahashi, Yoshikazu Tanaka*, and Takeshi Yokoyama*. 
    Direct visualization of ribosomes in the cell-free system revealed the functional evolution of aminoglycoside. 
    J Biochem (2024) 
     
  3. Xuewei Zhao, Ding Ma, Kensuke Ishiguro, Hironori Saito, Shinichiro Akichika, Ikuya Matsuzawa, Mari Mito, Toru Irie, Kota Ishibashi, Kimi Wakabayashi, Yuriko Sakaguchi, Takeshi Yokoyama, Yuichiro Mishima, Mikako Shirouzu, Shintaro Iwasaki, Takeo Suzuki*, and Tsutomu Suzuki*
    Glycosylation of queuosine in tRNAs contributes to optimal translation and post-embryonic growth in vertebrates 
    Cell 186(25) 5517-5535 (2023) 
     
  4. Chisa Shiraishi, Akinobu Matsumoto*, Kazuya Ichihara, Taishi Yamamoto, Takeshi Yokoyama, Taisuke Mizoo, Atsushi Hatano, Masaki Matsumoto, Yoshikazu Tanaka, Eriko Matsuura-Suzuki, Shintaro Iwasaki, Shouji Matsushima, Hiroyuki Tsutsui, Keiichi I. Nakayama*
    RPL3L-containing ribosomes determine translation elongation dynamics required for cardiac function. 
    Nature Communications 14(1):2131 (2023)
     
  5. Yuko Murayama, Haruhiko Ehara, Mari Aoki, Mie Goto, Takeshi Yokoyama, Shun-ichi Sekine. 
    Structural basis of the transcription termination factor Rho engagement with transcribing RNA polymerase. 
    Science Advances. 9(6) eade7093 (2023)
     
  6. Hiromi Watari, Hiromu Kageyama, Nami Masubuchi, Hiroya Nakajima, Kako Onodera, Pamela J. Focia, Takumi Oshiro, Takashi Matsui, Yoshio Kodera, Tomohisa Ogawa, Takeshi Yokoyama, Makoto Hirayama, Kanji Hori, Douglas M. Freymann, Misa Imai, Norio Komatsu, Marito Araki*, Yoshikazu Tanaka*, Ryuichi Sakai*
    A marine sponge-derived lectin reveals hidden pathway for thrombopoietin receptor activation. 
    Nature Communications 13(1) (2022)
     
  7. Yoshiko Nakagawa, Howard C.-H. Shen, Yusuke Komi, Shinju Sugiyama, Takaaki Kurinomaru, Yuri Tomabechi, Elena Krayukhina, Kenji Okamoto, Takeshi Yokoyama, Mikako Shirouzu, Susumu Uchiyama, Megumi Inaba, Tatsuya Niwa, Yasushi Sako, Hideki Taguchi, Motomasa Tanaka
    Amyloid conformation-dependent disaggregation in a reconstituted yeast prion system. 
    Nature Chemical Biology 18(3):321-331. (2022)
     
  8. Mutsuko Kukimoto-Niino, Kazushige Katsura, Rahul Kaushik, Haruhiko Ehara, Takeshi Yokoyama, Tomomi Uchikubo-Kamo, Reiko Nakagawa, Chiemi Mishima-Tsumagari, Mayumi Yonemochi, Mariko Ikeda, Kazuharu Hanada, Kam Y. J. Zhang, Mikako Shirouzu
    Cryo-EM structure of the human ELMO1-DOCK5-Rac1 complex
    Science Advances 7(30) eabg3147 (2021)
     
  9. Rie Umeda, Yuhkoh Satouh, Mizuki Takemoto, Yoshiko Nakada-Nakura, Kehong Liu, Takeshi Yokoyama, Mikako Shirouzu, So Iwata, Norimichi Nomura, Ken Sato, Masahito Ikawa, Tomohiro Nishizawa, Osamu Nureki
    Structural insights into tetraspanin CD9 function
    Nature Communications 11(1) (2020)
     
  10. Takeshi Yokoyama#, Kodai Machida#, Wakana Iwasaki#, Tomoaki Shigeta, Madoka Nishimoto, Mari Takahashi, Ayako Sakamoto, Mayumi Yonemochi, Yoshie Harada, Hideki Shigematsu, Mikako Shirouzu, Hisashi Tadakuma*, Hiroaki Imataka*, Takuhiro Ito*
    HCV IRES Captures an Actively Translating 80S Ribosome
    Molecular Cell 74(6) 1205-1214.e8 (2019)
    #equal contribution
     
  11. Yongchan Lee, Pattama Wiriyasermkul, Chunhuan Jin, Lili Quan, Ryuichi Ohgaki, Suguru Okuda, Tsukasa Kusakizako, Tomohiro Nishizawa, Kazumasa Oda, Ryuichiro Ishitani, Takeshi Yokoyama, Takanori Nakane, Mikako Shirouzu, Hitoshi Endou, Shushi Nagamori, Yoshikatsu Kanai, Osamu Nureki
    Cryo-EM structure of the human L-type amino acid transporter 1 in complex with glycoprotein CD98hc
    Nature Structural & Molecular Biology 26(6) 510-517 (2019)
     
  12. Kazuhiro Kashiwagi, Takeshi Yokoyama, Madoka Nishimoto, Mari Takahashi, Ayako Sakamoto, Mayumi Yonemochi, Mikako Shirouzu, Takuhiro Ito
    Structural basis for eIF2B inhibition in integrated stress response
    Science 364(6439) 495-499 (2019)
     
  13. Go Kasuya#, Takanori Nakane#, Takeshi Yokoyama#, Yanyan Jia, Masato Inoue, Kengo Watanabe, Ryoki Nakamura, Tomohiro Nishizawa, Tsukasa Kusakizako, Akihisa Tsutsumi, Haruaki Yanagisawa, Naoshi Dohmae, Motoyuki Hattori, Hidenori Ichijo, Zhiqiang Yan, Masahide Kikkawa, Mikako Shirouzu, Ryuichiro Ishitani*, Osamu Nureki*
    Cryo-EM structures of the human volume-regulated anion channel LRRC8
    Nature Structural & Molecular Biology 25(9) 797-804 (2018) 
    #equal contribution
     
  14. Haruhiko Ehara, Takeshi Yokoyama, Hideki Shigematsu, Shigeyuki Yokoyama, Mikako Shirouzu, Shun-ichi Sekine
    Structure of the complete elongation complex of RNA polymerase II with basal factors
    Science 357(6354) 921-924 (2017)
     
  15. Takeshi Yokoyama, Tanvir R Shaikh, Nobuhiro Iwakura, Hideko Kaji, Akira Kaji, Rajendra K Agrawal
    Structural insights into initial and intermediate steps of the ribosome-recycling process
    The EMBO Journal 31(7) 1836-1846 (2012)
     
  16. Takeshi Yokoyama, Tsutomu Suzuki
    Ribosomal RNAs are tolerant toward genetic insertions: evolutionary origin of the expansion segments
    Nucleic Acids Research 36(11) 3539-3551 (2008)
Activities in Academic Societies
The Japanese Society of Microscopy
Protein Science Society of Japan
The Biophysical Society of Japan
The RNA Society of Japan
The Molecular Biology Society of Japan

Recent Activities

Cryo-electron microscopy is the technique to observe biomolecules using the transmission electron microscope at liquid nitrogen temperature. Specimens are embedded in victorious ice layer by rapid freezing and observed in TEM. I have focused on ribosomal complexes related to novel antibiotics and translation regulation mechanism. Currently, sample preparations are performed in Tohoku University and subsequently cryo-EM data collections are performed in EM facilities in Japan.
 

Message to Students

It is exciting to see biomolecules in your interest using electron microscope. Research activity is sometimes hard but let’s do our research to pave the way for new discoveries !

Research