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Monitoring and kinetic analysis of the molecular interactions by which a repressor protein, PhaR, binds to target DNAs and poly[(R)-3-hydroxybutyrate]

Miwa Yamada14, Shuntaro Takahashi25, Yoshio Okahata2, Yoshiharu Doi3 and Keiji Numata1*

Author Affiliations

1 Enzyme Research Team, RIKEN Biomass Engineering Program, RIKEN, 2-1, Hirosawa, Wako-shi, Saitama, 351-0198, Japan

2 Department of Biomolecular Engineering, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan

3 Research Cluster for Innovation, RIKEN, 2-1, Hirosawa, Wako-shi, Saitama, 351-0198, Japan

4 Present address: Department of Biological Chemistry and Food Science, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, 020-8550, Japan

5 Present address: Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan

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AMB Express 2013, 3:6  doi:10.1186/2191-0855-3-6

Published: 27 January 2013


The repressor protein PhaR, which is a component of poly[(R)-3-hydroxybutyrate] granules, functions as a repressor of the gene expression of the phasin PhaP and of PhaR itself. We used a quartz crystal microbalance to investigate the binding behavior by which PhaR in Ralstonia eutropha H16 targets DNAs and amorphous poly[(R)-3-hydroxybutyrate] thin films. Binding rate constants, dissociation rate constants, and dissociation constants of the binding of PhaR to DNA and to amorphous poly[(R)-3-hydroxybutyrate] suggested that PhaR bind to both in a similar manner. On the basis of the binding rate constant values, we proposed that the phaP gene would be derepressed in harmony with the ratio of the concentration of the target DNA to the concentration of amorphous poly[(R)-3-hydroxybutyrate] at the start of poly[(R)-3-hydroxybutyrate] synthesis in R. eutropha H16.

Polyhydroxyalkanoate; Autoregulator protein PhaR; Kinetic analysis; Ralstonia eutropha H16