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B. Active state

FIGURE 9.25 Looping of DNA in RpoN-dependent Promoter

The sites for binding of transcription factors and the alternative sigma factor, RpoN, are shown in A. The IHF protein induces a bend in the DNA, which brings the NtrC sites close to the binding site for the alternative sigma factor RpoN. Because the DNA loops around, the RNA poly merase can be bound by two sets of NtrC dimers as well as by the RpoN protein.

DNA may be bent into a loop by some regulatory proteins.

and IHF are examples of proteins that are involved in bending DNA (as opposed to H-NS, which binds to DNA already bent as a result of its sequence; see Ch. 4). They help in integration, inversion and recombination events by bending DNA into the appropriate conformation (see Ch. 14).They also affect the expression of certain genes that need the DNA in their upstream regions to be bent, in order to be transcribed. A variety of other accessory proteins, activator proteins, and repressor proteins are also involved in the looping of DNA.

Many genes for nitrogen metabolism require the alternative sigma factor RpoN (= NtrA = o54) for their transcription. In addition, they are regulated by activator proteins that bind far upstream. Most activator proteins, at least in bacteria, bind just upstream of the promoter and make direct contact with RNA polymerase, so helping it bind to the promoter. For the activators of RpoN-dependent promoters to touch the RNA polymerase, the DNA must be bent around, forming a loop. The bend results from IHF binding between the promoter and activator sites (Fig. 9.25).

Genes for using many alternative nitrogen sources are regulated by the NtrBC two-component regulatory system; although NtrB is not a membrane protein as is typically the case (see above). In the absence of ammonia, the NtrB protein phospho-rylates NtrC protein. NtrC-P then binds to the upstream region of nitrogen-source genes and activates transcription. Similarly, the genes for nitrogen fixation, in Klebsiella and related bacteria, require the RpoN sigma factor and the activator NifA. In both cases, IHF must bend the DNA into a loop for activation to work.

The enhancers that activate eukaryotic promoters also act at a distance and depend on looping of DNA (see Ch. 10). Because of this similarity, the activator sites of RpoN-dependent promoters have sometimes been called bacteria enhancers. However, the bacterial activator sites are only about 100 bp upstream and occupy a fixed position. In contrast, eukaryotic enhancers may lie several kilobases upstream or downstream of their target genes, and can work in either orientation.

In genetics there are examples of anti-everything—including anti-termination.

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