Abstract
The E. coli chromosome is compacted by segregation into 400–500 supercoiled domains by both active and passive mechanisms, for example, transcription and DNA-protein association. We find that prophage Mu is organized as a stable domain bounded by the proximal location of Mu termini L and R, which are 37 kbp apart on the Mu genome. Formation/maintenance of the Mu ‘domain’ configuration, reported by Cre-loxP recombination and 3C (chromosome conformation capture), is dependent on a strong gyrase site (SGS) at the center of Mu, the Mu L end and MuB protein, and the E. coli nucleoid proteins IHF, Fis and HU. The Mu domain was observed at two different chromosomal locations tested. By contrast, prophage λ does not form an independent domain. The establishment/maintenance of the Mu domain was promoted by low-level transcription from two phage promoters, one of which was domain dependent. We propose that the domain confers transposition readiness to Mu by fostering topological requirements of the reaction and the proximity of Mu ends. The potential benefits to the host cell from a subset of proteins expressed by the prophage may in turn help its long-term stability.
Highlights
Bacterial chromatin is spatially organized and condensed,1000 fold to fit inside a bacterial cell [1]
We show in this study that the 37 kbp transposable prophage Mu exists in a unique configuration we call the ‘Mu domain’, where its two ends are paired, segregating the Mu sequences from those of the host chromosome
This is the largest stable chromosomal domain in E. coli mapped to date
Summary
Bacterial chromatin is spatially organized and condensed ,1000 fold to fit inside a bacterial cell [1]. Referred to as a nucleoid, E. coli chromatin is organized in a series of negatively supercoiled loops [2,3], segregated by dynamic domain barriers (defined as entities that prevent the free diffusion of supercoils) and compacted by several nucleoid-associated proteins (NAPs) including HU, IHF, Fis and H-NS [4,5]. Segregation of supercoils into topological domains protects these processes by preventing DNA breaks from relaxing the entire chromosome [2,8]. The level of DNA superhelicity is tightly controlled by the combined activities of topoisomerases and histone-like proteins; the latter constrain negative supercoils and generate diffusion barriers for the formation of topological domains, but are global regulators of gene transcription [4,9,10,11]. The critical importance of DNA supercoiling in interconnecting chromosome structure and global gene transcription was reinforced in recent evolution experiments where supercoiling was observed to be under strong selection in E. coli populations [12]
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