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one) are outside this region and are transcribed directly from and PL (which stand for rightward and leftward promoter, respectively), or from other promoters whose activities are controlled by products of genes transcribed from PR and PLi. PRM [promoter for repressor maintenance) transcribes only the cl gene. PR and PL are strong, constitutive promoters-—that is, they bind RNA polymerase efficiently and direct transcription without help from an activator. PKM, in contrast, is a weak promoter and only directs efficient transcription when an activator is bound just upstream. PRM resembles the lac promoter in this regard.

There are two arrangements of gene expression depicted in Figure 16-27: one renders growth lytic, the other lysogenic. Lytic growth proceeds when PL and PR remain switched on, while PBM is kept off. Lysogenic growth, in contrast, is a consequence of PL and PK being switched off, and P^m switched on. How are these promoters controlled?

tetrsmerization activating, region tetrsmerization activating, region dimenzation

DMA binding dimenzation

DMA binding

FIGURE 16-28 Ji repressor, the figure shows a monomer of X repressor, indicating various surfaces involved in diffcit'nt. activities earned out by the protein. N indicates the ¿mino domain, C the carboxy domain. "Tetrameniation" denotes the region where two dimers interact when binding cooperatively to adjacent sites on 1JNA (Source: Adapted trom Pteshne M and Cann A. 2002. Cones 8 signals, p. 36, Fig 1-17. © Cold Spring Harbor Laboratory Press.)

Regulatory Proteins and Their Binding Sites

The cl gene encodes X repressor, a protein of two domains joined by a flexible linker region (Figure 16-28). The N-terminal domain contains the DNA-binding region (a helix-turn-helix domain, as we saw earlier). As with the majority of DNA-binding proteins, \ repressor binds DNA as a dimer; the main dimwization contacts are made between the C-terminai domains. A single dimer recognizes a 17 bp DNA sequence, each monomer recognizing one half-site, again just as wo saw in the lac system. (We have already looked at the details of DNA recognition by \ repressor in Figure 16-12.)

Despite its name, \ repressor can both activate and repress transcription. When functioning as a repressor, it works in the same way as does Lac repressor—it binds to sites that overlap the promoter and excludes RNA polymerase. As an activator, \ repressor works like CAP, by recruitment. \ repressor's activating region is in the N-terminal domain of the protein, its target on polymerase is a region of the ct subunit adjacent to the part of n that recognizes the -35 region of the promoter [region 4, see Chapter 12, Figure 12-6),

Cro (which stands for control of repressor and other things) only represses transcription, like Lac repressor. It is a single domain protein and again binds as a dimer to 17 bp DNA sequences.

k repressor anrl Cro can each bind to any one of six operators. These sites are recognized with different affinities by each of the proteins. Three of those sites are found in the left-control region, and three in the right. We will focus on the binding of K repressor and Cro to the sites in the right-hand region, and these are shown in Figure 16-29. Binding to sites in the left-hand control region follows a similar pattern.

The three binding sites in the right operator are called 0R1, 0R7, and CV,; these sites are similar in sequence, but not identical, and each one—if isolated from the others and examined separately—can bind

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