title: Structural change of DNA induced by nucleoid proteins: growth phase-specific Fis and stationary phase-specific Dps.
abstract: The effects of nucleoid proteins Fis and Dps of Escherichia coli on the higher order structure of a giant DNA were studied, in which Fis and Dps are known to be expressed mainly in the exponential growth phase and stationary phase, respectively. Fis causes loose shrinking of the higher order structure of a genome-sized DNA, T4 DNA (166 kbp), in a cooperative manner, that is, the DNA conformational transition proceeds through the appearance of a bimodal size distribution or the coexistence of elongated coil and shrunken globular states. The effective volume of the loosely shrunken state induced by Fis is 30-60 times larger than that of the compact state induced by spermidine, suggesting that cellular enzymes can access for DNA with the shrunken state but cannot for the compact state. Interestingly, Dps tends to inhibit the Fis-induced shrinkage of DNA, but promotes DNA compaction in the presence of spermidine. These characteristic effects of nucleotide proteins on a giant DNA are discussed by adopting a simple theoretical model with a mean-field approximation.
authors: Department of Physics, Kyoto University, Kyoto, Japan.
authors: Yuko T
authors: YT
authors: Sato
authors: Shun
authors: S
authors: Watanabe
authors: Takahiro
authors: T
authors: Kenmotsu
authors: Masatoshi
authors: M
authors: Ichikawa
authors: Yuko
authors: Y
authors: Yoshikawa
authors: Jun
authors: J
authors: Teramoto
authors: Tadayuki
authors: T
authors: Imanaka
authors: Akira
authors: A
authors: Ishihama
authors: Kenichi
authors: K
authors: Yoshikawa
mesh_terms: D001425:Bacterial Outer Membrane Proteins / Q000378:metabolism*; D017122:Bacteriophage T4; D049109:Cell Proliferation / Q000187:drug effects; D055598:Chemical Phenomena; D004279:DNA, Viral / Q000737:chemistry* / Q000378:metabolism*; D004926:Escherichia coli / Q000166:cytology* / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000378:metabolism*; D035021:Factor For Inversion Stimulation Protein / Q000378:metabolism*; D042541:Intracellular Space / Q000378:metabolism; D009690:Nucleic Acid Conformation / Q000187:drug effects; D011073:Polyamines / Q000378:metabolism; D011485:Protein Binding; D013095:Spermidine / Q000494:pharmacology
chemical_list: D001425:Bacterial Outer Membrane Proteins; D004279:DNA, Viral; D029968:Escherichia coli Proteins; D035021:Factor For Inversion Stimulation Protein; C501034:Fis protein, E coli; D011073:Polyamines; C088010:dps protein, E coli; D013095:Spermidine
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