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Functomics Biology I Research Team
Akeo SHINKAI
Team Leader
Akeo SHINKAI (Ph.D.)
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Research Areas

Transcription reaction is the initial step of the central dogma, and this reaction is performed by RNA polymerase. In order to adapt to environmental changes, it is positively or negatively regulated by proteins called transcription factors. The aim of our study is to understand fundamental transcriptional newtork system and to observe the phenotype as the results of transcriptional changes by means of SPring-8 beamline or XFEL technology using extremely thermophilic bacterium Thermus thermophilus HB8 as a model organism. This approach is useful to find functions of about 500 kinds of functionally unknown proteins in this organisms.

Research Subject

  1. Structural and functional analysis of transcription factor from Thermus thermophilus HB8
  2. Basic studies for single-cell imaging
  3. Molecular imaging of CRISPR/Cas system, a nobel antivirus system of prokaryote

Related links

  1. RIKEN SPring-8 Center Website_Laboratories PageNew Window
  2. Structual-Biological Whole Cell Project PageNew Window

RIKEN RESEARCH

December 26, 2008
The recession gene
A master switch allows bacteria, already living in extreme environments, to survive times of crisis New Window

List of Selected Publications

  1. Agari, Y., Kuramitsu, S., Shinkai, A.:
    "Crystal structure of hypothetical protein TTHB210, controlled by the sigmaE/anti-sigmaE regulatory system in Thermus thermophilus HB8, reveals a novel homodecamer"
    Proteins, 80, 958-962 (2012)
  2. Sakamoto, K., Agari, Y., Kuramitsu, S., Shinkai, A.:
    "Phenylacetyl-coenzyme A is an effector molecule of TetR family transcriptional repressor PaaR from Thermus thermophilus HB8"
    J. Bacteriol., 193, 4388-4395 (2011)
  3. Agari, Y., Agari, K., Sakamoto, K., Kuramitsu, S., Shinkai, A.:
    "TetR family transcriptional repressor FadR controls fatty acid degradation"
    Microbiology, 157, 1589-1601 (2011)
  4. Sakamoto, K., Agari, Y., Agari, K., Kuramitsu, S., Shinkai, A.:
    "Structural and functional characterization of transcriptional repressor CsoR from Thermus thermophilus HB8"
    Microbiology, 156, 1993-2005 (2010)
  5. Agari, Y., Sakamoto, K., Tamakoshi, M., Oshima, T., Kuramitsu, S., Shinkai, A.:
    "Transcription profile of Thermus thermophilus CRISPR systems after phage infection"
    J. Mol. Biol., 395, 270-281 (2010)
  6. Sakamoto, K., Agari, Y., Agari, K., Yokoyama, S., Kuramitsu, S., Shinkai, A.:
    "X-ray crystal structure of a CRISPR-associated RAMP superfamily protein, Cmr5, from Thermus thermophilus HB8"
    Proteins, 75, 528-532 (2009)
  7. Agari, Y., Yokoyama, S., Kuramitsu, S., Shinkai, A.:
    "X-ray crystal structure of a CRISPR-associated protein, Cse2, from Thermus thermophilus HB8"
    Proteins, 73, 1063-1067 (2008)
  8. Agari, Y., Kashihara, A., Yokoyama, S., Kuramitsu, S., Shinkai, A.:
    "Global gene expression mediated by Thermus thermophilus SdrP, a CRP/FNR family transcriptional regulator"
    Mol. Microbiol., 70, 60-75 (2008)
  9. Shinkai, A., Ohbayashi, N., Terada, T., Shirouzu, M., Kuramitsu, S., Yokoyama, S.:
    "Identification of promoters recognized by RNA polymerase-sigmaE holoenzyme from Thermus thermophilus HB8"
    J. Bacteriol., 189, 8758-8764 (2007)
  10. Shinkai, A., Kira, S., Nakagawa, N., Kashihara, A., Kuramitsu, S., Yokoyama, S.:
    "Transcription activation mediated by a cyclic AMP receptor protein from Thermus thermophilus HB8"
    J. Bacteriol., 189, 3891-3901 (2007)

Members

Principal Investigator

Akeo SHINKAI
Team Leader

Postdoctoral Fellow

Yoshihiro AGARI
Postdoctoral Researcher
Keiko SAKAMOTO
Research Associate
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