Figure 1. (a) DNA is a plectonemic helix (left) rather than a paranemic helix (right), and thus it must spin axially to undergo replication, transcription and extended pairing for homologous recombination. Supercoiling in circular bacterial chromosomes is maintained by the concerted action of DNA gyrase, which introduces negative supercoils at the expense of adenosine triphosphate (ATP) binding and hydrolysis, and TopoI plus TopoII, which remove excess negative supercoils. Negative supercoiled DNA adopts an interwound conformation. However, ‘solenoidal’ supercoils can be stabilized when DNA is wrapped on a protein surface. This is the mechanism of supercoil formation in mammalian cells (centre left). Most bacteria have nonspecific DNA-binding proteins such as HU and H-NS, which stabilize supercoils but are much less effective at condensing DNA compared with true histones (centre right). (b) Bacteria and eukaryotes both have an enzyme, TopoIV and TopoII, respectively, designed to unknot and untangle DNA.

Figure 2. (a) A replication fork is shown with a replisome as a blue box, moving and synthesizing DNA from left to right. Replication is semi-conservative, meaning that a new strand is synthesized on each of the two parental template strands; and semi-discontinuous, meaning that the strand that follows the fork with 5¢ to 3¢ polarity is made as one continuous piece while the strand that follows with overall 3¢ to 5¢ polarity is made discontinuously as Okazaki pieces. (b) The two circular chromosomes show the products of bidirectional replication. Initiation starts at oriC (–85) and proceeds clockwise in the zone called replichore I and counter-clockwise through the zone called replichore II. Replication forks meet at a terminus near the dif site (–34). Strands made in the continuous mode are shown in red, and discontinuous strands in blue. Also included in the map are the seven ribosomal RNA operons (arrowheads), five of which reside in replichore I and two of which are found in replichore II, six ter sites and the dif site. Note that the two daughters are synthesized with different semi-discontinuous styles in replichores II and I so that the Watson and Crick strands are isomers.

Figure 3. Structure and replication pattern of a eukaryotic chromosome. Eukaryotic chromosomes are linear structures with special structures at each end called telomeres (green) and an organizer centre called the centromere, which attaches the chromosome to the spindle during chromosome segregation. Replication is initiated at Ars sites, and replication is carried out semi-discontinuously so that the two strands are replication isomers.

Figure 4. Topology of DNA replication. Movement of a replication fork produces positive supercoiling ahead of the fork and results in entanglements of the sister chromosomes, called catenanes, behind the fork. Positive supercoils are removed by gyrase in bacteria and by TopoI in eukaryotes, whereas TopoIV resolves catenanes in bacteria and TopoII in eukaryotes.

Figure 5. Nucleoid formation in E. coli. After initiation at oriC, the origin regions (O) migrates to the cell 1.4 and 3.4 positions where they remain as the cell grows. The two arms of replichore I are supercoiled and then deposited to on outer edges of the newly forming nucleoids. The arms from replichore II are supercoiled and deposited at the inner margin of the growing nucleoids. The terminus is last to replicate and it is located between the two nucleoids at the mid-cell site of cell division.

Figure 6. Chromosome segregation in eukaryotes is completed in the mitotic cycle. Mitosis proceeds through four stages, prophase, metaphase, anaphase and telophase, as described in the text. At anaphase, the cohesins which were attached to bind each sister chromosome together are cleaved to allow movement of each bivalent to opposite cell poles. Then the nuclear membrane is re-established and the cell cycle can begin again.

Figure 7. Organization of highly transcribed genes in E. coli and Sal. typhimurium. The genetic map position of the most actively transcribed 27 protein-encoding genes from E. coli (inner map) and Salmonella (outer map) are shown in black. The messenger RNA transcript abundance (RNA/DNA ratio) measured by microarray analysis listed after each gene. Brackets show the boundary of an inversion at the terminus of DNA replication. During growth in rich medium, the seven ribosomal RNA operons shown in blue dominate the transcription landscape. 70% of all RNA polymerase molecules are engaged in production of stable RNAs for ribosomes and tRNA.