Principles of Gene Regulation:- Transcription Initiation Is Regulated by Proteins That Bind to or near Promoters
At least three types of proteins regulate transcription initiation by RNA polymerase: specificity factors alter the specificity of RNA polymerase for a given promoter or set of promoters; repressors impede access of RNA polymerase to the promoter; and activators enhance the RNA polymerase–promoter interaction. although we did not refer to them by that name. The σ subunit of the E. coli RNA polymerase holoenzyme is a specificity factor that mediates promoter recognition and binding. Most E. coli promoters are recognized by a single σ subunit (Mr 70,000), σ70. Under some conditions, some of the σ70 subunits are replaced by another specificity factor. One notable case arises when the bacteria are subjected to heat stress, leading to the replacement of 70 by σ32 (Mr 32,000). When bound to σ32, RNA polymerase is directed to a specialized set of promoters with a different consensus sequence (Fig. 1). These promoters control the ex pression of a set of genes that encode the heat-shock response proteins. Thus, through changes in the binding affinity of the polymerase that direct it to different promoters, a set of genes involved in related processes is co ordinately regulated. In eukaryotic cells, some of the general transcription factors, in particular the TATA-binding protein (TBP; see Fig. 26–8), may be considered specificity factors.
Repressors bind to specific sites on the DNA. In prokaryotic cells, such binding sites, called operators, are generally near a promoter. RNA polymerase binding, or its movement along the DNA after binding, is blocked when the repressor is present. Regulation by means of a repressor protein that blocks transcription is referred to as negative regulation. Repressor binding to DNA is regulated by a molecular signal (or effector), usually a small molecule or a protein, that binds to the repressor and causes a conformational change. The interaction between repressor and signal molecule either increases or decreases transcription. In some cases, the conformational change results in dissociation of a DNA-bound repressor from the operator (Fig. 2a). Transcription initiation can then proceed unhindered. In other cases, interaction between an inactive repressor and the signal molecule causes the repressor to bind to the operator (Fig. 2b). In eukaryotic cells, the binding site for a repressor may be some distance from the promoter; binding has the same effect as in bacterial cells: inhibit ing the assembly or activity of a transcription complex at the promoter. Activators provide a molecular counterpoint to re pressors; they bind to DNA and enhance the activity of RNA polymerase at a promoter; this is positive regulation. Activator binding sites are often adjacent to promoters that are bound weakly or not at all by RNA polymerase alone, such that little transcription occurs in the absence of the activator. Some eukaryotic activators bind to DNA sites, called enhancers, that are quite distant from the promoter, affecting the rate of transcription at a promoter that may be located thousands of base pairs away. Some activators are normally bound to DNA, enhancing transcription until dissociation of the activator is triggered by the binding of a signal molecule (Fig. 2c). In other cases the activator binds to DNA only after interaction with a signal molecule (Fig. 2d). Signal molecules can therefore increase or decrease transcription, depending on how they affect the activator. Positive regulation is particularly common in eukaryotes, as we shall see.
FIGURE 1 Consensus sequence for promoters that regulate expression of the E. coli heat shock genes. This system responds to temperature increases as well as some other environmental stresses, resulting in the induction of a set of proteins. Binding of RNA polymerase to heat-shock promoters is mediated by a specialized subunit of the polymerase, σ32, which replaces σ70 in the RNA polymerase initiation complex.
FIGURE 2 Common patterns of regulation of transcription initiation. Two types of negative regulation are illustrated. (a) Repressor (pink) binds to the operator in the absence of the molecular signal; the external signal causes dissociation of the repressor to permit tran scription. (b) Repressor binds in the presence of the signal; the re pressor dissociates and transcription ensues when the signal is re moved. Positive regulation is mediated by gene activators. Again, two types are shown. (c) Activator (green) binds in the absence of the molecular signal and transcription proceeds; when the signal is added, the activator dissociates and transcription is inhibited. (d) Activator binds in the presence of the signal; it dissociates only when the signal is removed. Note that “positive” and “negative” regulation refer to the type of regulatory protein involved: the bound protein either facilitates or inhibits transcription. In either case, addition of the molecular signal may increase or decrease transcription, depending on its effect on the regulatory protein.
