DNA replication divides the circular Escherichia coli chromosome into equal arms (replichores). Visualization of pairwise combinations of multiple genetic loci reveals that the two replichores occupy separate nucleoid halves, with the replication origin between; positions of loci on each replichore recapitulate the genetic map. Sequential replication-segregation regenerates the structure by sequentially layering newly replicated replichore DNA to specific inner and outer edges of the developing sister nucleoids. Replication fork-dependent locus positions are imprinted, so that in most generations the chromosome orientation in a mother cell is recreated as a arrangement of sister chromosomes in daughter cells. Although it has been known for many years that bacterial circular chromosomes are replicated bidirectionally from a defined origin, precisely how this DNA is organized into the bacterial nucleoid, and how and when chromosomal DNA is segregated, has remained elusive (Sherratt 2003;Wu 2004;Gitai et al. 2005). Replication divides the chromosome into two equal arms (replichores), each being transcribed predominantly in the same direction as replication, and each containing distinctive asymmetric base-skewed DNA sequences that are important for chromosome processing (Blattner et al. 1997;Rocha 2004;Lesterlin et al. 2005). In recent years a combination of improved cytological methods, in which specific genetic loci were visualized using either fluorescent in situ hybridization (FISH), or the binding of fluorescent DNA-binding proteins to their cognate DNAbinding sites (FROS), have begun to reveal that bacterial chromosomes are highly organized yet dynamic structures (e.g., see Gordon et al. 1997;Niki et al. 2000;Li et al. 2002;Bates and Kleckner 2005;Wang et al. 2005), with DNA replication apparently being confined to specific cellular "replication factories" (Lemon and Grossman 2000;Adachi et al. 2005;Bates and Kleckner 2005).Models of chromosome organization based on these analyses for Escherichia coli, Bacillus subtilis, and Caulobacter crescentus have favored an arrangement in which the ori-ter chromosome axis runs longitudinally along the cell, with left and right chromosome arms (replichores) placed above and below this axis, or interwound (Teleman et al. 1998;Niki et al. 2000;Viollier et al. 2004;Gitai et al. 2005;Thanbichler et al. 2005). Such an organization is clear in C. crescentus, where in a resting cell, the replication origin region, ori, localizes to one cell pole, and ter, the replication termination region, to the other pole, and other loci lie between the two. Sequential replication-segregation generates two daughter cells that are mirror symmetrical with respect to chromosome orientation ( Fig. 1; Viollier et al. 2004;Gitai et al. 2005). The E. coli data have provided conflicting views of how DNA is organized in vivo and how/when it segregates. Nevertheless, the idea of chromosome organization about a longitudinal axis has been implicit (Niki a...
