Publications

Publication:”An Assembly Intermediate Structure of Rice Dwarf Virus Reveals a Hierarchical Outer Capsid Shell Assembly Mechanism”

Dr. Yusuke Nakamichi, Mr. Kenta Tsutsumi, Dr. Akifumi Higashiura of Nakagawa Lab. and Dr. Naoyuki Miyazaki of Takagi Lab. and their collaborators revealed intermediate structure during self-assembly process of Rice dwarf virus using cryo-electron microscopy with phase plate.

   Many viruses are covered with shells of proteins that have an icosahedral structure which are known for the pattern of a soccer ball. The Reoviridae viruses have a distinctive structure further covered with a multilayered shell (capsid) of a different pattern. Rotavirus that causes infant diarrhea is well known as an example. We succeeded to reveal the formation of multilayered capsids with different patterns in Rice Dwarf Virus (RDV), one of the Reoviridae viruses, by genetic engineering technology and phase-contrast cryo-electron microscopy.

   RDV is covered with icosahedral capsids of two different patterns called T = 1 (inner shell) and T = 13 (outer capsid). In this study, we coupled green fluorescent protein (GFP) to the outer capsid protein using genetic recombination technology and used it to form virus particles. As a result, RDV particles with an incomplete shell was created by the sterically hinderance of GFP. A phase-contrast cryo-electron microscopy revealed that the outer capsid proteins of RDV bind only to a specific region of the inner capsid (on the three-fold axes). It was found that the outer shell protein of RDV is firstly bound on the three-rotational axes of the inner shell, and other pouter capsid proteins are sequentially inserted on the beside of the initially bound proteins so as to combine the pieces of the puzzle.

   This result revealed how the reovirus particles with multilayered shells are formed for the first time. In addition, by using this result to efficiently inhibit particle formation, it is expected to be applicable to the prevention of infectious diseases and development of therapeutic drugs. This research project was conducted in collaboration with Dr. Kazuyoshi Murata of National Institute for Physiological Sciences. Okazaki, Japan.

Publication:
An Assembly Intermediate Structure of Rice Dwarf Virus Reveals a Hierarchical Outer Capsid Shell Assembly Mechanism, Yusuke Nakamichi, Naoyuki Miyazaki, Kenta Tsutsumi, Akifumi Higashiura, Hirotaka Narita, Kazuyoshi Murata, Atsushi Nakagawa, Structure, 27(3), 439-448, 2019
doi: https://doi.org/10.1016/j.str.2018.10.029

This paper is downloadable from the following URL until April 24, 2019.

https://authors.elsevier.com/a/1YgIa3SNvbqscV

Publication:“Phosphorylation of an intrinsically disordered region of Ets1 shifts a multi-modal interaction ensemble to an auto-inhibitory state”

On 4th January 2018, a paper has been published from Nucleic Acids Research (IF=10.162) by the research team of Dr. Kota Kasahara (Ritsumeikan University), Dr. Masaaki Shiina, Prof. Kazuhiro Ogata (Yokohama City University), Prof. Junichi Higo and Prof. Haruki Nakamura (IPR, Osaka University), revealing the regulation mechanism of the intrinsically disordered region of Ets1 transcription factor due to phosphorylation of Ser residues by molecular simulation and biochemical studies.

 

Click here for more details

 

Publication: “Subtelomeres constitute a safeguard for gene expression and chromosome homeostasis”

Nucleic Acids Research Breakthrough article describes the biological role of subtelomeric sequences in chromosome maintenance and chromatin structure.

Research teams led by Dr. Junko Kanoh at Osaka University and by Kunihiro Ohta at the University of Tokyo (Japan), have described a study of the biological function of subtelomeric homologous (SH) sequences (and of subtelomeres more generally) through phenotypic analysis of a Schizosaccharomyces pombe (fission yeast) mutant in which all SH sequences in the genome were deleted.

 

NAR_Breakthrough.pdf

 

 

A paper by Dr. Gert-Jan Bekker has been published from Journal of Chemical Theory and Computation with its cover picture of the Issue 7, 2017.

A paper”Accurate Prediction of Complex Structure and Affinity for a Flexible Protein Receptor and its Inhibitor (http://pubs.acs.org/doi/abs/10.1021/acs.jctc.6b01127, DOI: 10.1021/acs.jctc.6b01127) by Dr. Gert-Jan Bekker, who is a Specially Appointed Assistant Professor in IPR, has been published from Journal of Chemical Theory and Computation (JCTC, IF=5.301) with its cover picture of the Issue 7, 2017.

 

Figure.jpg

Press Release: Calredoxin, a novel protein for promoting efficient photosynthesis

Outline

A group of researchers reports on the structure and function of a novel protein named “Calredoxin”. Calredoxin binds calcium and catalyzes in dependence of its binding, redox reactions, particularly driving the detoxification of harmful oxygen species. The researchers are exploring how this protein functions at the crossroad of calcium- and redox-dependent reactions to promote efficient oxygenic photosynthesis.

Shugoshin forms a specialized chromatin domain at subtelomeres that regulates transcription and replication timing.

A chromosome is composed of structurally and functionally distinct domains. However, the molecular mechanisms underlying the formation of chromatin structure and the function of subtelomeres, the telomere-adjacent regions, remain obscure. Here we report the roles of the conserved centromeric protein Shugoshin 2 (Sgo2) in defining chromatin structure and functions of the subtelomeres in the fission yeast Schizosaccharomyces pombe.

Received the Most-downloaded Publication Award Q3 2015! Closed-cycle cold helium magic-angle spinning for sensitivity-enhanced multi-dimensional solid-state NMR

・Magic-angle spinning (MAS) NMR probe system with a closed-loop helium recirculation.
・Stable MAS for weeks at sample temperature T = 35 K without consuming helium.
・Multi-dimensional MAS NMR at T = 35 K at a low running cost for electricity 16 kW/h.
・An order of magnitude sensitivity gain at T = 40 K and B0 = 16.4 T.

Selective oxidation of 5-hydroxymethylcytosine with micelle incarcerated oxidants to determine it at single base resolution.

5-Methylcytosine (5mC) is oxidized by ten-eleven translocation (TET) enzymes. This process followed by thymine DNA glycosylase is proposed to be the mechanism for methylcytosine demethylation. 5-Hydroxymethylcytosine (5hmC) is one of the most important key oxidative metabolites in the demethylation process, and therefore, simple and accurate method to determine 5hmC at single base resolution is desired. In the present study, we developed a mild catalytic oxidation of 5-hmC using micelle incarcerated oxidants that enables to determine the position of 5hmC at single base resolution.