Regulating Gene Expression

To cope with changing conditions in their environment, microorganisms have evolved elaborate control mechanisms to synthesize the maximum amount of cell material from a limited supply of energy. This is critical, because generally a microorganism must reproduce more rapidly than its competitors in order to be successful.

Consider the situation of Escherichia coli. For over 100 million years, it has successfully inhabited the gut of mammals, where it reaches concentrations of 106 cells per milliliter. In this habitat, it must cope with alternating periods of feast and famine. For a limited time after a mammal eats, E. coli in the large intestine prosper, wallowing in the milieu of amino acids, vitamins, and other nutrients. The cells actively take up these compounds they would otherwise synthesize, expending minimal energy. Simultaneously, the cells shut down their biosynthetic pathways, channeling the conserved energy into the rapid synthesis of macromolecules, including DNA, RNA, and protein. Under these conditions, the cells divide at their most rapid rate. Famine, however, follows the feast. Between meals, which may be many days in the case of some mammals, the rich source of nutrients is depleted. Now the cells' biosynthetic pathways must be activated, using energy and markedly slowing cell division. Cells dividing several times an hour in a nutrient-rich environment may divide only once every 24 hours in a famished mammalian gut.

A cell controls its metabolic pathways by two general mechanisms. The most immediate of these is the allosteric inhibition of enzymes. The most energy-efficient strategy, however, is to control the actual synthesis of the enzymes, making only what is required. To do this, cells have the ability to control expression of certain genes. ■ allosteric regulation, p. 140

Principles of Regulation

Not all genes are subjected to the same type of regulation. Many are routinely expressed, whereas others are either turned on or off by certain conditions. Enzymes are often described according to characteristics of the regulation that governs their synthesis:

■ Constitutive enzymes are constantly synthesized; the genes that encode these enzymes are always active.

7.6 Regulating Gene Expression 183

Constitutive enzymes usually play indispensable roles in the central metabolic pathways. For example, the enzymes of glycolysis are constitutive. ■ central metabolic pathways, p. 142

■ Inducible enzymes are not regularly produced; instead, their synthesis is turned on by certain conditions. Inducible enzymes are often involved in the utilization of specific energy sources. A cell would waste precious resources if it synthesized the enzyme when the energy source is not present. An example of an inducible enzyme is /i-galactosidase, whose sole function is to break down the disaccharide lactose into its two component monosaccharides, glucose and galactose. The mechanisms by which the cell controls b-galactosidase synthesis serve as an important model for regulation and will be described shortly.

■ Repressible enzymes are routinely synthesized, but they can be turned off by certain conditions. Repressible enzymes are generally involved in biosynthetic pathways, such as those that produce amino acids. Cells require a sufficient amount of a given amino acid to multiply; thus, the amino acid must be either synthesized or available as a component of the growth medium. If a certain amino acid is not present in the medium, then the cell must synthesize the enzymes involved in its manufacture. When the amino acid is supplied, however, synthesis of the enzymes would waste energy.

Mechanisms to Control Transcription

The mechanisms that a cell uses to prevent or facilitate transcription must be readily reversible, allowing cells to effectively control the relative number of transcripts made. In some cases, the control mechanisms may affect the transcription of only a limited number of genes; in other cases, a wide array of genes is coordinately controlled. For example, in E. coli the expression of more than 300 different genes is affected by the availability of glucose as an energy source. The simultaneous regulation of numerous genes unrelated in function is called global control.

Transcription of genes is often controlled by means of a regulatory region near the promoter to which a specific protein can bind, acting as a sophisticated on/off switch. When a regulatory protein binds to DNA, it can either act as a repressor, which blocks transcription, or an activator, which facilitates transcription. A set of adjacent genes coordinately controlled by a regulatory protein and transcribed as a single polycistronic message is called an operon.

Repressors

A repressor is a regulatory protein that blocks transcription. It does this by binding to DNA at a region, called the operator, located immediately downstream of a promoter. This effectively prevents RNA polymerase from progressing past that region to initiate transcription. Regulation involving a repressor is called negative control.

184 Chapter 7 The Blueprint of Life, from DNA to Protein

Specific molecules may bind to the repressor and, by doing so, alter the ability of the repressor to bind to DNA. This can occur because repressors are allosteric proteins, having a distinct site to which another molecule can bind. When that molecule binds, the shape of the repressor is altered. In turn, this affects the ability of the repressor to bind to DNA. As shown in figure 7.18, there are two general mechanisms by which different repressors can function:

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