Figure 1. The gal promoter in Escherichia coli. (a) The location of the two overlapping promoters P1 (+1) and P2 (–5), two operators, O_E (–60.5) and O_I (+53.5), HU-binding site (hbs) at +6.5, and the 5¢ region of the first structural gene, galE. (b) Looping-mediated repression of the gal promoters by GalR–GalR interactions (red) in the presence of HU (green). The elements are not drawn to scale.

Figure 2. Effect of Gal repressor (GalR) and the histone like protein HU on the repression of the gal promoters (P1 and P2) in a purified system containing DNA template, RNA polymerase, GalR and HU. Lanes 1–6, DNA template with wild-type operators; lanes 7–8, mutant O_I; and lanes 9–10, mutant O_E. RNA1 transcripts are from a control promoter. Reprinted with permission from Aki and Adhya (1997). Copyright © 1997 Oxford University Press.

Figure 3. Electron micrograph of DNA looping by LacI bound to two lac operators engineered into O_E and O_I loci of the gal operon of Escherichia coli. The arrows point to the DNA loops. Reprinted with permission from Mandal et al., (1990). Copyright © 1990 Cold Spring Harbor Laboratory Press.

Figure 4. Repression of galP2 in vivo. The strength of the promoter P2 was monitored by measuring the level of a reporter gene (gusA) product -glucuronidase. (a) In the presence (green) and absence (black) of inducer d-galactose (I). (b) In the presence (red) and absence (black) of coumermycin (C). (c) In the presence and absence of HU; blue, mutated in hupA and hupB genes encoding the and subunits of HU, respectively; green, mutated in hupA; red, mutated in hupB. The arrow indicates the point at which d-galactose or coumermycin was added. Reprinted with permission from Lewis et al. (1999). Copyright © 1999 Blackwell Science Ltd.

Figure 5. Models of HU in DNA looping. GalR (red), HU (green). (a) HU acts as a DNA bender; (b) HU acts both as a bender and an adaptor. hbs, HU-binding site.

Figure 6. Repression of the lac promoter. (a) The locations of the lac operators, O₁ (+11), O₂ (+402) and O₃ (–92) with respect to the transcription start site of +1 for the lac promoter (P_lac). The 5¢ region of the lacZ gene is included. (b) DNA looping by the binding of LacI to O₁ and O₂. (c) DNA looping by the binding of LacI to O₁ and O₃.

Figure 7. DNA looping at the ara promoter (P_BAD). (a) The location of half-sites O₂ (–275), I₁ (–64) and I₂ (–43) with respect to the transcription start site of promoter. The 5¢ region of the araB structural gene is included. (b) The binding of AraC (red) to O₂ and I₁ in the absence of inducer (l-arabinose) forms a DNA loop. The binding of AraC (green) to I₁ and I₂ in the presence of inducer destroys DNA looping and activates P_BAD.

Figure 8. Periodicity in the repression of the promoter at the ara operon. The periodicity oscillates between repression and derepression depending on the distance between O₂ and I₁. Reprinted with permission from Lee and Schleif (1989). Copyright © 1989 National Academy of Sciences, USA.

Figure 9. DNA looping at the promoters of glnA, glnH and nifH. (a) The enhancer binding sites of the nitrogen regulatory protein NtrC are located at –140 and –110 upstream of the p2 promoter of the gln ALG operon of Escherichia coli. (b) DNA looping for activation of p2 by the interaction of NtrCP (green) bound to the enhancer sites and ⁵⁴ RNA polymerase (RNAP) (red) bound to the promoter. (c) The spatial relationship of the enhancer site (–132) and the integration host factor (IHF) site (–56) with respect to the promoter (p) of the nif HDK operon. (d) DNA looping at the nif HDK operon by the binding of IHF (blue), NifA (green) and ⁵⁴ RNA polymerase (red) to their respective binding sites. (e) The spatial relationship of enhancer sites (–121 and –108) and the IHF site (–42) with respect to the promoter (p2) of the gln HPQ operon. (f) DNA looping at the gln HPQ operon by the binding of IHF (blue), NtrCP (green) and ⁵⁴ RNA polymerase (red) to their respective binding sites.

Figure 10. Schematic diagram of the Escherichia coli chromosome showing loop domain structures during DNA compaction. Reprinted with permission from Trun and Marko. (1998) Copyright © 1998.