Linear ordering and dynamic segregation of the bacterial chromosome

Organization is a hallmark of life (1). As observational methods have improved, the extent of organization that is revealed has grown continuously. It was once thought that the bacterial nucleoid might be the last refuge of entropy because of its amorphous appearance in micrographs. This view was undermined by the demonstration that a few specific sequences, such as the origin and terminus of replication, were at least roughly localized within the cell (2–4). Several other regions of the chromosome were also found to reside between the origin and terminus, suggesting that the arrangement of chromosomal loci in the cell might correspond to their order along the DNA (5, 6). Now, in a technical tour de force from the Shapiro and McAdams laboratories at Stanford presented in this issue of PNAS, Viollier et al. (7) studied 112 sites across the genome of Caulobacter crescentus and found that every one has a specific location within the nucleoid. They accomplished this feat by using the fluorescent repressor–operator system (FROS), in which an array of transcriptional operators inserted into the chromosome is illuminated by means of a fluorescent derivative of the cognate repressor (2, 8, 9).

The pattern is perfectly simple (Fig. 1A1). In resting G₁ cells, the cellular position of any gene correlates linearly with how far it is along the chromosome from the replication origin. Thus, genes close to the origin localize near the origin at one cell pole, those genetically near the terminus are near the opposite cell pole, and the rest are ordered in between. Because replication proceeds bidirectionally from the origin, the pattern also reflects replication timing, with origin-proximal loci being replicated earliest. Equally dramatic live-cell imaging demonstrated that, after replication, loci segregate actively to mirror-symmetric positions (Fig. 1 A2). The two …