DNA phase transition promoted by replication initiator.
DNA is flexible and easily subjected to bending and wrapping via DNA/protein interaction. DNA supercoiling is known to play an important role in a variety of cellular events, such as transcription, replication, and recombination. It is, however, not well understood how the superhelical strain is efficiently redistributed during these reactions. Here we demonstrate a novel property of an initiator protein in DNA relaxation by utilizing a one-molecule-imaging technique, atomic force microscopy, combined with biochemical procedures. A replication initiator protein, RepE54 of bacterial mini-F plasmid (2.5 kb), binds to the specific sequences (iterons) within the replication region (ori2). When RepE54 binds to the iterons of the negatively supercoiled mini-F plasmid, it induces a dynamic structural transition of the plasmid to a relaxed state. This initiator-induced relaxation is mediated neither by the introduction of a DNA strand break nor by a local melting of the DNA double strand. Furthermore, RepE54 is not wrapped by DNA repeatedly. These data indicate that a local strain imposed by initiator binding can induce a drastic shift of the DNA conformation from a supercoiled to a relaxed state.
Yoshimura
S H
SH
Graduate School of Biostudies and Department of Genetics and Molecular Biology, Institute for Virus Research, Kyoto University, Japan. yoshimur@gaia.h.kyoto-u.ac.jp
Ohniwa
R L
RL
Sato
M H
MH
Matsunaga
F
F
Kobayashi
G
G
Uga
H
H
Wada
C
C
Takeyasu
K
K
D000255:Adenosine Triphosphate / Q000737:chemistry; D001426:Bacterial Proteins / Q000737:chemistry* / Q000648:ultrastructure; D004265:DNA Helicases / Q000737:chemistry* / Q000648:ultrastructure; D004261:DNA Replication; D004264:DNA Topoisomerases, Type I / Q000737:chemistry; D004269:DNA, Bacterial / Q000737:chemistry* / Q000648:ultrastructure; D004270:DNA, Circular / Q000737:chemistry; D004278:DNA, Superhelical / Q000737:chemistry / Q000648:ultrastructure; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000648:ultrastructure; D029968:Escherichia coli Proteins; D005144:F Factor / Q000737:chemistry; D018625:Microscopy, Atomic Force; D009698:Nucleoproteins / Q000737:chemistry; D010957:Plasmids / Q000737:chemistry / Q000648:ultrastructure; D011485:Protein Binding; D012097:Repressor Proteins / Q000737:chemistry* / Q000648:ultrastructure; D015534:Trans-Activators / Q000737:chemistry* / Q000648:ultrastructure
D001426:Bacterial Proteins; D004269:DNA, Bacterial; D004270:DNA, Circular; D004278:DNA, Superhelical; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; D009698:Nucleoproteins; C074164:RepE protein, E coli; D012097:Repressor Proteins; D015534:Trans-Activators; C045264:replication initiator protein; D000255:Adenosine Triphosphate; D004265:DNA Helicases; D004264:DNA Topoisomerases, Type I