DNA Looping and Transcription Regulation


DNA loops, formed by the association of two proteins while bound to spatially separated specific DNA sites, control gene transcription negatively or positively. DNA looping sometimes needs an architectural protein, which acts by bending the DNA segment that loops.

Keywords: enhancer; repressor; operator; nucleoid; GalR; AraC; NtrC; repressosome

Figure 1.

The gal promoter in Escherichia coli. (a) The location of the two overlapping promoters P1 (+1) and P2 (−5), two operators, OE (−60.5) and OI (+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 OI; and lanes 9–10, mutant OE. RNA1 transcripts are from a control promoter. Reprinted with permission from Aki and Adhya . Copyright © 1997 Oxford University Press.

Figure 3.

Electron micrograph of DNA looping by LacI bound to two lac operators engineered into OE and OI loci of the gal operon of Escherichia coli. The arrows point to the DNA loops. Reprinted with permission from Mandal et al., . 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 β‐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 α and β 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.. 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 (Plac). 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 (PBAD). (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 PBAD.

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 . 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 σ54 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 σ54RNA 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 σ54RNA 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. Copyright © 1998.



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Further Reading

Adhya S, Geanacopoulos M, Lewis DEA, Roy S and Aki T (1998) Transcription regulation by repressosome and RNA polymerase contact. Cold Spring Harbor Symposia on Quantitative Biology 63: 1–9.

Collado‐Vides J, Magasanik B and Gralla JD (1991) Control site location and transcriptional regulation in Escherichia coli. Microbiological Reviews 55: 371–394.

Kustu S, Santero E, Keener J, Popham D and Weiss D (1989) Expression of σ54 (ntr A)‐dependent genes is probably united by a common mechanism. Microbiological Reviews 53: 367–376.

Martin K, Huo L and Schleif RF (1986) The DNA loop model for ara repression: AraC protein occupies the proposed loop sites in vivo and repression‐negative mutations lie in the same sites. Proceedings of the National Academy of Sciences of the USA 83: 3654–3658.

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Lewis, Dale EA, and Adhya, Sankar(Dec 2001) DNA Looping and Transcription Regulation. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0000851]