Chromosome Organization by a Nucleoid-Associated Protein in Live Bacteria

Abstract

We used super-resolution fluorescence microscopy and chromosome-conformation capture assay to study the distributions of major nucleoid-associated proteins in live Escherichia coli cells. HU, Fis, IHF, and StpA were largely scattered throughout the nucleoid. In contrast, H-NS, a global transcriptional silencer, formed two compact clusters per chromosome, driven by oligomerization of DNA-bound H-NS through interactions mediated by the amino-terminal domain of the protein. H-NS sequestered the regulated operons into these clusters and juxtaposed numerous DNA segments broadly distributed throughout the chromosome. Deleting H-NS led to substantial chromosome reorganization. These observations demonstrate that H-NS plays a key role in global chromosome organization in bacteria.