Chapter 11 : DNA Supercoiling and Its Consequences for Chromosome Structure and Function

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Gyrase was the first type II enzyme discovered, and it remains unique for its ability to introduce negative supercoils into relaxed, positively or negatively supercoiled DNA at the expense of ATP binding and hydrolysis. An essential enzyme in bacteria, gyrase is critical for nearly all complex transactions that involve DNA, including recombination, replication, transcription, and chromosome segregation. The homeostatic supercoil regulation model was inspired by two observations. First, many promoters sense supercoiling levels. Second, expression of gyrase increases when the chromosome becomes relaxed, whereas the expression of topo I requires high supercoiling levels. Chromosome replication has three critical stages (initiation, elongation, and segregation), each with different supercoiling problems. For initiation, the two strands of must separate to allow assembly of the replication machinery (the replisome). Transcription encompasses supercoiling problems similar in two respects to those of replication. First, transcription initiation requires unpairing of the DNA duplex, and supercoiling can influence this step as it does in initiation of DNA replication. Second, transcription is similar to replication in that movement of RNA polymerase generates temporary positive supercoiling ahead of, and negative supercoiling behind, the DNA segment that is being transcribed. The torsional effects of transcription have been studied with supercoil-sensitive promoters by measuring the formation of Z-DNA and by monitoring the extrusion of cruciforms. Homologous and site-specific genetic recombination, adaptive mutation, "supercoil regulated" gene transcription, gene order on chromosomes, and plasmid-chromosome replication segregation are all phenomena that are likely to be influenced by DNA dynamics.

Citation: Higgins N. 1999. DNA Supercoiling and Its Consequences for Chromosome Structure and Function, p 189-202. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch11
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Image of FIGURE 1

The difference between plectonemic and paranemic helices is that strand separation of a plectonemic molecule requires twisting about the long axis.

Citation: Higgins N. 1999. DNA Supercoiling and Its Consequences for Chromosome Structure and Function, p 189-202. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch11
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Image of FIGURE 2

Plectonemic movement required for δ resolution. At the top, the organization of the γδ resolvase binding site is given along with three sub-sites labeled , and . Each subsite binds a dimer of resolvase, but only resolvase dimers bound at the subsite can catalyze DNA strand exchange. Following binding, the two sites must form a precise synapse, which tangles the six subsites into three interwound supercoils. Two movements of DNA allow this juxtapositioning: slithering, in which DNA moves like a conveyor belt and all points along the chain move relative to all other points, and supercoil branch migration, in which extrusion and résorption of supercoil branches cause sites to become plectonemically interwound. The recombination products include a deletion (shown as a shaded circle), which is initially catenated with the chromosome but which is released by the activity of topo IV.

Citation: Higgins N. 1999. DNA Supercoiling and Its Consequences for Chromosome Structure and Function, p 189-202. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch11
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Image of FIGURE 3

The domain size distribution of exponentially growing cultures of in the 43-to 45-min () segment of the chromosome. The curve is a right skewed distribution, with a median size of 40 kb; less than 10% of the cells have domains under 2 kb, and about 5% of the cells have 80-kb domains. Below the graph is an illustration of how the domains might be cordoned off by barriers. For a 20-kb domain with 60 to 75 interwound supercoils, all sites in the red zone communicate and sequences in the blue zone do not. A 40-kb domain has at least one less barrier, and the 80-kb domain has no barriers, so all sites can communicate through slithering and supercoil branch migration.

Citation: Higgins N. 1999. DNA Supercoiling and Its Consequences for Chromosome Structure and Function, p 189-202. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch11
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