Fundamental structural units of the Escherichia coli nucleoid revealed by atomic force microscopy

A small container of several to a few hundred mm3 (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 sub-jected 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 ®brous structure with a diameter of ~80 nm was found. In addition to this `80 nm ®ber', a thinner `40 nm ®ber' and a higher order `loop ' structure were identi®ed in the log phase nucleoid. In the later growth phases, the nucleoid turned into a `coral reef structure ' that also possessed the 80 nm ®ber units, and, ®nally, 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 pre-viously available information, we propose a struc-tural model of the E.coli nucleoid