This chapter summarizes recent evidence about the composition, structures, and function of components that form supercoil domains in bacterial nucleoids. Nucleoid formation enables a cell to move a compact DNA ensemble of dynamic transcription complexes and multiple replisomes efficiently into daughter cells during the cell division. In the past 10 years advances were made in many bacterial systems, but this review focuses on work carried out in the closely related clades of Escherichia coli and Salmonella typhimurium. New information indicates most of the chromosome has a stochastic domain structure but that transcription organizes unique topological zones in a small fraction of the genome. Nucleoid formation becomes critical when cells constrict the cell cycle to carry out dichotomous replication. Under very short doubling times of dichotomous growth, cell division requires intricate coordination of multiple factors to promote chromosome segregation. The most crucial enzyme for nucleoid formation is DNA gyrase, which not only removes positive links during DNA replication, it also establishes the supercoil tension that promotes correct compaction. Important enzymes including Topo IV, FtsK, and XerCD recombinases are tuned to promote nucleoid segregation only when appropriate levels of supercoiling are present. Surprisingly, gyrase establishes significantly different supercoiling levels in E. coli and Salmonella typhimurium, which makes the enzyme a barrier for horizontal gene transfer between the species.
