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Multiscale Structuring of the E. coli Chromosome by Nucleoid-Associated and Condensin Proteins

Lioy, Virginia S., Cournac, Axel, Marbouty, Martial, Duigou, Stéphane, Mozziconacci, Julien, Espéli, Olivier, Boccard, Frédéric, Koszul, Romain
Cell 2018 v.172 no.4 pp. 771-783.e18
DNA, Escherichia coli, chromosomes, eukaryotic cells, genome, proteins, replication origin
As in eukaryotes, bacterial genomes are not randomly folded. Bacterial genetic information is generally carried on a circular chromosome with a single origin of replication from which two replication forks proceed bidirectionally toward the opposite terminus region. Here, we investigate the higher-order architecture of the Escherichia coli genome, showing its partition into two structurally distinct entities by a complex and intertwined network of contacts: the replication terminus (ter) region and the rest of the chromosome. Outside of ter, the condensin MukBEF and the ubiquitous nucleoid-associated protein (NAP) HU promote DNA contacts in the megabase range. Within ter, the MatP protein prevents MukBEF activity, and contacts are restricted to ∼280 kb, creating a domain with distinct structural properties. We also show how other NAPs contribute to nucleoid organization, such as H-NS, which restricts short-range interactions. Combined, these results reveal the contributions of major evolutionarily conserved proteins in a bacterial chromosome organization.