coli In most bacteria, DNA is present in supercoiled form. The circular nature of the E. coli chromosome makes it topologically constrained molecule that is mostly negatively supercoiled with an estimated average supercoiling density (σ) of -0.05. In the eukaryotic chromatin, DNA is found mainly in the toroidal form that is restrained and defined by histones through the formation of nucleosomes. In contrast, in the E. coli nucleoid, about half of the chromosomal DNA is organized in the form of free, plectonemic supercoils. The remaining DNA is restrained in either the plectonemic form or alternative forms, including but not limited to the toroidal form, by interaction with proteins such as NAPs. Thus, plectonemic supercoils represent effective supercoiling of the E. coli genome that is responsible for its condensation and organization. Both plectonemic and toroidal supercoiling aid in DNA condensation. It is noteworthy that because of branching of plectonemic structures, it provides less DNA condensation than does the toroidal structure. A same size DNA molecule with equal supercoiling densities is more compact in a toroidal form than in a plectonemic form. In addition to condensing DNA, supercoiling aids in DNA organization. It promotes disentanglement of DNA by reducing the probability of catenation. Supercoiling also helps bring two distant sites of DNA in proximity thereby promoting a potential functional interaction between different segments of DNA. Sources of supercoiling in E. coli Three factors contribute to generating and maintaining chromosomal DNA supercoiling in E. coli: (i) activities of topoisomerases, (ii) the act of transcription, and (iii) NAPs. Topoisomerases Topoisomerases are a particular category of DNA metabolic enzymes that create or remove supercoiling by breaking and then re-ligating DNA strands. E. coli possesses four topoisomerases. DNA gyrase introduces negative supercoiling in the presence of ATP and it removes positive supercoiling in the absence of ATP. Across all forms of life, DNA gyrase is the only topoisomerase that can create negative supercoiling and it is because of this unique ability that bacterial genomes possess free negative supercoils; DNA gyrase is found in all bacteria but absent from higher eukaryotes. In contrast, Topo I opposes DNA gyrase by relaxing the negatively supercoiled DNA. There is genetic evidence to suggest that a balance between the opposing activities of DNA gyrase and Topo I are responsible for maintaining a steady-state level of average negative superhelicity in E. coli. Both enzymes are essential for E. coli survival. A null