11).
Genes whose products regulate the expression of other genes are called regulatory genes. The product of a regulatory gene can either inhibit or stimulate the expression of a gene. If it inhibits expression, the regulation is negative; if it stimulates expression, the regulation is positive. Some regulatory gene products are both positive and negative regulators depending on the situation. The product of a regulatory gene can regulate the expression of only one other gene, or it can regulate the expression of many genes. The set of genes regulated by the same regulatory gene product is called a regulon. If a gene product regulates its own expression, it is said to be autoregulated. We discuss the molecular mechanisms of regulation of gene expression in much more detail in chapter 11, but in this chapter, we briefly review some basic concepts needed to understand the following chapters.
Figure 2.42 The sortase A pathway. (A) Typical sortase substrate. The protein is composed of an N-terminal signal peptide and a C-terminal cell wall-sorting signal (Cws). The Cws contains a conserved LPXTG motif followed by a hydrophobic stretch of amino acids and positively charged residues at the C terminus. (B) Model for the cell wall sortase A pathway in Staphylococcus aureus. (1) The full-length surface protein precursor is secreted through the cytoplasmic membrane via an N-terminal signal sequence. (2) A charged tail (+) at the C terminus of the protein may serve as a stop transfer signal. Following cleavage of this secretion signal, a sortase enzyme cleaves the protein between the threonine and glycine residues of the LPXTG motif, forming a thioacyl-enzyme intermediate to a specific cysteine in the sortase (3). It is then attached to the free amine of the five-glycine cross-bridge of lipid II (4) before transfer into the cell wall (5). The Pro-Gly-Ser-Thr region may help it through the thick cell wall so that it is expressed on the cell surface. PP is the site of MurNAc pentapeptide attachment to bactoprenyl in the membrane in lipid II. Modified from Connolly KM, Clubb RT, in Waksman G, Caparon M, Hultgren S (ed), Structural Biology of Bacterial Pathogenesis (ASM Press, Washington, DC, 2005).
Transcriptional Regulation
Expression of a gene is often regulated by controlling the amount of mRNA that is made from the gene. This is called transcriptional regulation. It makes sense to regulate gene expression at this level, as it is wasteful to make mRNAs if the expression of the gene is going to be inhibited at a later stage. Also, bacterial genes are often arranged in a polycistronic unit, or operon; if the genes in this unit are involved in a related function, they can all be regulated simultaneously by regulating the synthesis of the polycistronic mRNA of that operon.
Regulation of transcription of an operon usually occurs at the initial stages of transcription, at the promoter. Whether or not a gene is expressed depends on whether the promoter for the gene is used to make mRNA. Transcriptional regulation at the promoter for a gene can be determined by specific recognition of the promoter by RNA polymerase holoenzyme containing an alternative sigma factor. Regulation can also use regulatory proteins that can act either negatively or positively, depending on whether the regulatory gene product is a transcriptional repressor or a transcriptional activator, respectively. The difference between regulation of transcription by repressors and activators is illustrated in Figure 2.43. A repressor binds to the DNA at an operator sequence close to, or even overlapping, the promoter and prevents RNA polymerase from using the promoter, often by physically obstructing access to the promoter by the RNA polymerase. An activator, in contrast, usually binds upstream of the promoter at an activator site, where it can help the RNA polymerase bind to the promoter or help open the promoter after the RNA polymerase binds. Sometimes, a transcriptional regulator can be a repressor on some promoters and an activator on other promoters, depending on where it binds relative to the start site of transcription.
Figure 2.43 (A) The two general types of transcriptional regulation. In negative regulation, a repressor binds to a repressor-binding site (or operator) and turns expression of the operon off. In positive regulation, an activator protein binds upstream of the promoter and turns expression of the operon on. (B) Graph showing the most common locations of activator sites relative to repressor sites. Activator sites are usually farther upstream. Each data point indicates the middle of the known region on the DNA where a regulatory protein binds. Zero on the x axis marks the start point of transcription. Modified from Collado-Vides J, Magasanik B, Gralla JD, Microbiol Rev 55:371–394, 1991.
The activity of a regulatory protein can itself be modified by the binding of small molecules called effectors which affect its activity (note that the term effector is also used for proteins that are translocated by pathogens into eukaryotic cells). Effectors used in gene regulation are often molecules that can be used by the cell if the regulated operon is expressed or essential metabolites that do not have to be made by the cell if their concentration is already high. If the small-molecule effector causes transcription of the operon to be turned on (for example, by binding to a repressor and changing its structure so that the repressor can no longer bind to the DNA), the small molecule is called an inducer. If binding of the effector to a repressor causes the operon to be turned off, the small molecule is called a corepressor. The activity of regulatory proteins can also be modulated by posttranslational modification (e.g., phosphorylation [see Box 12.3]) or by interaction with other proteins or RNAs.
Not all transcriptional regulation occurs at the promoter, however. Sometimes transcription starts and then stops prematurely, resulting in synthesis of a truncated mRNA that does not include the protein-coding sequence. Such regulation is called attenuation of transcription. These and other mechanisms of transcriptional regulation are discussed in subsequent chapters.
Posttranscriptional Regulation
Expression of a gene can be regulated at later stages in gene expression (see chapter 11). For example, the mRNA may be degraded by RNases as soon as it is made, before it can be translated. In translational regulation, translation of the mRNA can be regulated to determine how much of the protein product is made. Posttranslational regulation results in regulation of the activity of a protein product of a gene by degradation by proteases or modifications, such as phosphorylation or methylation, depending on the conditions in which the cell finds itself. In addition, the product of a pathway may inhibit the activity of an enzyme in the pathway by a process called feedback inhibition. In general, a type of regulation of gene expression that operates after the mRNA for a gene has been made is called posttranscriptional regulation. Specific examples of posttranscriptional regulation are also discussed in subsequent chapters.