Atomic force microscopy analysis of the role of major DNA-binding proteins in organization of the nucleoid in Escherichia coli.
Bacterial genomic DNA is packed within the nucleoid of the cell along with various proteins and RNAs. We previously showed that the nucleoid in log phase cells consist of fibrous structures with diameters ranging from 30 to 80 nm, and that these structures, upon RNase A treatment, are converted into homogeneous thinner fibers with diameter of 10 nm. In this study, we investigated the role of major DNA-binding proteins in nucleoid organization by analyzing the nucleoid of mutant Escherichia coli strains lacking HU, IHF, H-NS, StpA, Fis, or Hfq using atomic force microscopy. Deletion of particular DNA-binding protein genes altered the nucleoid structure in different ways, but did not release the naked DNA even after the treatment with RNase A. This suggests that major DNA-binding proteins are involved in the formation of higher order structure once 10-nm fiber structure is built up from naked DNA.
Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, Tennoh-dai, Tsukuba, Ibaraki, Japan. ohniwa@md.tsukuba.ac.jp
Ryosuke L
RL
Ohniwa
Hiroki
H
Muchaku
Shinji
S
Saito
Chieko
C
Wada
Kazuya
K
Morikawa
D004264:DNA Topoisomerases, Type I / Q000737:chemistry / Q000378:metabolism; D004269:DNA, Bacterial / Q000737:chemistry / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D019286:Endopeptidase K / Q000737:chemistry / Q000378:metabolism; D004926:Escherichia coli / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism*; D018625:Microscopy, Atomic Force; D009154:Mutation
D004269:DNA, Bacterial; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; D019286:Endopeptidase K; D004264:DNA Topoisomerases, Type I