All transcription regulators, whether they are repressors or activators, must be bound to DNA to exert their effects. In this way, each regulatory protein acts selectively, controlling only those genes that bear a cis-regulatory sequence recognized by it. The logic of the Lac operon first attracted the attention of biologists more than 50 years ago. The way it works was uncovered by a combination of genetics and biochemistry, providing some of the first insights into how transcription is controlled in any organism.
We have seen that transcription activators help RNA polymerase initiate transcription and repressors hinder it. However, the two types of proteins are very similar to one another. For example, to occupy their cis-regulatory sequences, both the tryptophan repressor and the CAP activator protein must bind a small molecule; moreover, they both recognize their cis-regulatory sequences using the same structural motif (the helix–turn–helix shown in Panel 7–1). Indeed, some proteins (for example, the CAP protein) can act as both a repressor and an activator, depending on the exact placement of their cis-regulatory sequence relative to the promoter: for some genes, the CAP cis-regulatory sequence overlaps the promoter, and CAP binding thereby prevents the assembly of RNA polymerase at the promoter.
Most bacteria have small, compact genomes, and the cis-regulatory sequences that control the transcription of a gene are typically located very near to the start point of transcription. But there are some exceptions to this generalization— cis-regulatory sequences can be located hundreds and even thousands of nucleotide pairs from the bacterial genes they control (Figure 7–16). In these cases, the intervening DNA is looped out, allowing a protein bound at a distant site along the DNA to contact RNA polymerase. Here, the DNA acts as a tether, enormously increasing the probability that the proteins will collide, compared with the situation where one protein is bound to DNA and the other is free in solution. We will see shortly that, although it is the exception in bacteria, DNA looping occurs in the regulation of nearly every eukaryotic gene.
A possible explanation for this difference is based on evolutionary considerations. It has been proposed that the compact, simple genetic switches found in bacteria evolved in response to large population sizes where competition for growth put selective pressure on bacteria to maintain small genome sizes. In contrast, there appears to have been little selective pressure to “streamline” the genomes of multicellular organisms.
Figure 7–16 Transcriptional activation at a distance. (A) the ntrC protein is a bacterial transcription regulator that activates transcription by directly contacting rnA polymerase. (B) the interaction of ntrC and rnA polymerase, with the intervening DnA looped out, can be seen in the electron microscope. (B, courtesy of harrison echols and Sydney Kustu.)