Molecular and Chemical Life Science :
Chemical Biology


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

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.
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.

Selected Publications
  1. Umeda R, Satouh Y, Takemoto M, Nakada-Nakura Y, Liu K, Yokoyama T, Shirouzu M, Iwata S, Nomura N, Sato K, Ikawa M, Nishizawa T, Nureki. Structural insights into tetraspanin CD9 function. Nat Commun. 11:1606. (2020)
  2. Nakamura R, Numata T, Kasuya G, Yokoyama T, Nishizawa T, Kusakizako T, Kato T, Hagino T, Dohmae N, Inoue M, Watanabe K, Ichijo H, Kikkawa M, Shirouzu M, Jentsch TJ, Ishitani R, Okada Y, Nureki O. Cryo-EM structure of the volume-regulated anion channel LRRC8D isoform identifies features important for substrate permeation. Commun Biol. 3:240. (2020)
  3. Lee Y, Wiriyasermkul P, Jin C, Quan L, Ohgaki R, Okuda S, Kusakizako T, Nishizawa T, Oda K, Ishitani R, Yokoyama T, Nakane T, Shirouzu M, Endou H, Nagamori S, Kanai Y, Nureki O. Cryo-EM structure of the human L-type amino acid transporter 1 in complex with glycoprotein CD98hc. Nat Struct Mol Biol. 26(6):510-517. (2019).
  4. Yokoyama T*, Machida K*, Iwasaki W*, Shigeta T, Nishimoto M, Takahashi M, Sakamoto M, Yonemochi M, Harada Y, Shigematsu H, Shirouzu M, Tadakuma H, Imataka H, Ito T. HCV IRES captures an actively translating 80S ribosome. Mol Cell. 74(6):1205-1214. (2019). *equal contribution
  5. Kashiwagi K, Yokoyama T, Nishimoto M, Takahashi M, Sakamoto A, Yonemochi M, Shirouzu M, Ito T. Structural basis for eIF2B inhibition in integrated stress response. Science. 364(6439):495-499. (2019).
  6. Kasuya G*, Nakane T*, Yokoyama T*, Jia Y, Inoue M, Watanabe K, Nakamura R, Nishizawa T, Kusakizako T, Tsutsumi A, Yanagisawa H, Dohmae N, Hattori M, Ichijo H, Yan Z, Kikkawa M, Shirouzu M, Ishitani R, Nureki O. Cryo-EM structures of the human volume-regulated anion channel LRRC8. Nat Struct Mol Biol. 25(9):797-804. (2018). *equal contribution
  7. Chase AR, Laudermilch E, Wang J, Shigematsu H, Yokoyama T, Schlieker C. Dynamic functional assembly of the Torsin AAA+ ATPase and its modulation by LAP1. Mol Biol Cell. 28(21):2765-2772. (2017).
  8. Ehara H, Yokoyama T, Shigematsu H, Yokoyama S, Shirouzu M, Sekine SI. Structure of the complete elongation complex of RNA polymerase II with basal factors. Science. 357(6354):921-924. (2017).
  9. Iwakura N, Yokoyama T, Quaglia F, Mitsuoka K, Mio K, Shigematsu H, Shirouzu M, Kaji A, Kaji H. Chemical and structural characterization of a model Post-Termination Complex (PoTC) for the ribosome recycling reaction: Evidence for the release of the mRNA by RRF and EF-G. PLoS One. 12(5):e0177972. (2017).
  10. Yamagishi M, Shigematsu H, Yokoyama T, Kikkawa M, Sugawa M, Aoki M, Shirouzu M, Yajima J, Nitta R. Structural basis of backwards motion in kinesin-1-kinesin-14 chimera: implication for kinesin-14 motility. Structure, 24(8):1322-1334. (2016)
  11. Jeong H, Kim JS, Song S, Shigematsu H, Yokoyama T, Hyun J, Ha NC. Pseudoatomic structure of the tripartite multidrug efflux pump AcrAB-TolC reveals the intermeshing cogwheel-like interaction between AcrA and TolC. Structure, 24(2):272-6. (2016).
  12. Yokoyama T, Shaikh TR, Iwakura N, Kaji H, Kaji A, Agrawal RK. Structural insights into initial and intermediate steps of the ribosome-recycling process. EMBO J, 31, 1836-1846. (2012).
  13. Yokoyama T, Suzuki T. Ribosomal RNAs are tolerant toward genetic insertions :evolutionary origin of the expansion segments. Nucleic Acids Res. 36(11):3539-51. (2008).
Activities in Academic Societies
The Japanese Society of Microscopy
The RNA 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 !