Published online 1 April 2004
Nucleic Acids Research, 2004, Vol. 32, No. 6 1982-1992
© 2004 Oxford University Press
Fundamental structural units of the Escherichia coli nucleoid revealed by atomic force microscopy
Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan and 1 Division of Molecular Biology, Nippon Institute for Biological Science, Shinmachi, Ome, Tokyo 198-0024, Japan
*To whom correspondence should be addressed. Tel/Fax: +81 75 753 6852; Email: takeyasu{at}lif.kyoto-u.ac.jp
Received July 25, 2003; Revised December 25, 2003; Accepted March 9, 2004
A small container of several to a few hundred µm3 (i.e. bacterial cells and eukaryotic nuclei) contains extremely long genomic DNA (i.e. mm and m long, respectively) in a highly organized fashion. To understand how such genomic architecture could be achieved, Escherichia coli nucleoids were subjected to structural analyses under atomic force microscopy, and found to change their structure dynamically during cell growth, i.e. the nucleoid structure in the stationary phase was more tightly compacted than in the log phase. However, in both log and stationary phases, a fundamental fibrous structure with a diameter of 
80 nm was found. In addition to this ‘80 nm fiber’, a thinner ‘40 nm fiber’ and a higher order ‘loop’ structure were identified in the log phase nucleoid. In the later growth phases, the nucleoid turned into a ‘coral reef structure’ that also possessed the 80 nm fiber units, and, finally, into a ‘tightly compacted nucleoid’ that was stable in a mild lysis buffer. Mutant analysis demonstrated that these tight compactions of the nucleoid required a protein, Dps. From these results and previously available information, we propose a structural model of the E.coli nucleoid.
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