FY2020 Annual Report

Professor Matthias Wolf

Abstract

Fiscal year 2019 was characterized by very fruitful collaborations, including partners at Tokyo University, Osaka University, Hiroshima University, Nagasaki University, and at the University of Otago in New Zealand. Dr. Jaekyung Hyun, who brings extensive experience in cryo-EM, image processing and virology, joined the team. We were able to add several high-impact publications, including in the journals Nature Structural and Molecular Biology, Nature Microbiology and Philosophical Transactions of the Royal Society. The emphasis of the unit’s science has further been focused on molecular virology and molecular microbiology.

1. Staff

  •     Dr, Hideyuki Matsunami, Group Leader
  •     Dr. Satoshi Shibata, Staff Scientist
  •     Dr. Tae Gyun Kim, Staff Scientist
  •     Dr. Jaekyung Hyun, Staff Scientist
  •     Dr. Melissa Matthews, Postdoctoral Researcher
  •     Dr. Chloé Minnai, Postdoctoral Researcher
  •     Noriko Shibata, BSc, Technician (externally funded)
  •     Makoto Tokoro Schreiber, Graduate Student
  •     Keon Young, Graduate Student
  •     Rika Yoshizawa, Research Unit Administrator

2. Collaborations

2.1 Bacterial locomotion

  •     Type of collaboration: Joint research
  •     Researchers:
    • Professor Shin-Ichi Aizawa, Prefectural University of Hiroshima
    • Dr. Satoshi Shibata, Molecular Cryo-EM Unit, OIST
    • Dr. Hideyuki Matsunami, Molecular Cryo-EM Unit, OIST

2.2 Structure of bacterial adhesive pili

  •     Type of collaboration: Joint research
  •     Researchers:
    • Professor Koji Nakayama, University of Nagasaki
    • Professor Kazumi Imada, Osaka University
    • Assistant Professor Mikio Shoji, University of Nagasaki
    • Dr. Satoshi Shibata, Molecular Cryo-EM Unit, OIST
    • Dr. Hideyuki Matsunami, Molecular Cryo-EM Unit, OIST
    • Dr. Melissa Matthews, Molecular Cryo-EM Unit, OIST

2.3 Structure of Nucleosome complexes

  •     Type of collaboration: Joint research
  •     Researchers:
    • Professor Hitoshi Kurumizaka, University of Tokyo
    • Dr. Yoshimasa Takizawa, Molecular Cryo-EM Unit, OIST (now at Tokyo University)

2.4 Phage defense by CRISPR-CAS

  •     Type of collaboration: Joint research
  •     Researchers:
    • Professor Mihnea Bostina, University of Otago
    • Professor Peter Fineran, University of Otago

3. Activities and Findings

3.1 Structure of Bacterial Outer Membrane Porin Lamb

Figure 1. This is still work in progress by Dr. Tae Gyun Kim. The outer membrane protein (OMP) is a transmembrane protein that enables import and export of large cargo through the cell membrane.

3.2 CENP-A Trinucleosome

Figure 2. In this collaboration with the Kurumizaka Lab, first author Dr. Yoshimasa Takizawa reconstructed several states of in-vitro purified recombinant trinucleosomes from cryo-EM images collected in focus using a phase plate. The work suggests a model for the centromeric attachment site in the kinetochore, which is an essential property of chromosomes in cell division. The paper appeared in the journal Structure.

3.2 Strand exchange mechanism of major FimA pilus


Figure 3. By applying a similar image processing strategy as for the flagellar hook, first author Dr. Satoshi Shibata was able to reconstruct the pilus of the oral pathogen Porphyromonas gingivalis at near-atomic resolution. In collaboration with Prof. Imada at Osaka University, who solved atomic-resolution X-ray structures of the monomeric subunit, and the group of Prof. Nakayama at Nagasaki University, the joint team demonstrated experimentally for the first time the protease-mediated strand exchange mechanism of these adhesive pili. The work was published in Nature Microbiology.

 

4. Publications

 

4.1 Journals

4.2 Books and other one-time publications

Nothing to report

4.3 Oral and Poster Presentations

2020.02.27   Chromopalooza, Vienna, Austria, 1-2-3: mono-, di-, trinucleosomes and their impact on chromatin structure

2020.02.21   Meeting of the Japanese Pharmaceutical Manufacturer’s Association, OIST, Japan, Cryo-EM in Drug Design

2020.02.03   AMED BINDS Cryo-EM Workshop, OIST, Japan, Asymmetric reconstruction of filamentous proteins by single particle cryo-EM

2020               Shibata S, Hoji M, Matsunami H, Matthews M, Imada K, Nakayama K, Wolf M, Cryo-EM Structure of polymerized Type V pilus of P.gingivalis reveals assembly mechanism, 93th Japan Society of Bacteriology General Meeting 2020

5. Intellectual Property Rights and Other Specific Achievements

Nothing to report

6. Meetings and Events

Schreiber M.T., Wolf M.*, Measuring Dominant Local Structures in Amorphous Materials Using Nanobeam Electron Diffraction, Bulletin of the American Physical Society (2020), http://meetings.aps.org/Meeting/MAR20/Session/D10.7

Kim TG, Hyun J, Yu E, Wolf M.*, High-Resolution Architecture of Bacterial Outer Membrane Porin Lamb, Biophysical Journal 118 (3), 524a-525a, https://www.cell.com/biophysj/pdf/S0006-3495(19)33816-0.pdf

Schreiber M.T., Maigne A., Wolf M.* (2019). Charging Dynamics in Low-Dose Cryo-TEM Imaging. Microscopy and Microanalysis 25 (S2), 1004-1005, doi: 10.1017/S1431927619005750

 

7. Other

 

Nothing to report.