Genes VII

Positive and negative control systems are defined by the response of the operon when no regulator protein is present. The characteristics of the two types of control system are mirror images.

Genes under negative control are expressed unless they are switched off by a repressor protein (see Figure 10.2). Any action that interferes with gene expression can provide a negative control. Typically a repressor protein either binds to DNA to prevent RNA polymerase from initiating transcription, or binds to mRNA to prevent a ribosome from initiating translation.

Negative control provides a fail-safe mechanism: if the regulator protein is inactivated, the system functions and so the cell is not deprived of these enzymes. It is easy to see how this might evolve. Originally a system functions constitutively, but then cells able to interfere specifically with its expression acquire a selective advantage by virtue of their increased efficiency.

For genes under positive control, expression is possible only when an active regulator protein is present. The mechanism for controlling an individual operon is an exact counterpart of negative control, but instead of interfering with initiation, the regulator protein is essential for it. It interacts with DNA and with RNA polymerase to assist the initiation event (see Figure 10.3). A positive regulator protein that responds to a small molecule is usually called an activator. Other positive controls provide for the global substitution of sigma factors that change the selection of promoters (9 Transcription), or antitermination factors that change the recognition of terminators.

It is less obvious how positive control evolved, since the cell must have had the ability to express the regulated genes even before any control existed. Presumably some component of the control system must have changed its role. Perhaps originally it was used as a regular part of the apparatus for gene expression; then later it became restricted to act only in a particular system or systems.

Operons are defined as inducible or repressible by the nature of their response to the small molecule that regulates their expression. Inducible operons function only in the presence of the small-molecule inducer. Repressible operons function only in the absence of the small-molecule corepressor (so called to distinguish it from the repressor protein).

The terminology used for repressible systems describes the active state of the operon as derepressed; this has the same meaning as induced. The condition in which a (mutant) operon cannot be derepressed is sometimes called super-repressed; this is the exact counterpart of uninducible.

Either positive or negative control could be used to achieve either induction or repression by utilizing appropriate interactions between the regulator protein and the small-molecule inducer or corepressor. Figure 10.21 summarizes four simple types of control circuit. Induction is achieved when an inducer inactivates a repressor protein or activates an activator protein. Repression is accomplished when a corepressor activates a repressor protein or inactivates an activator protein.

The trp operon is a repressible system. Tryptophan is the end product of the reactions catalyzed by a series of biosynthetic enzymes. Both the activity and the synthesis of the tryptophan enzymes are controlled by the level of tryptophan in the cell.

Tryptophan functions as a corepressor that activates a repressor protein. This is the classic mechanism for repression, one of the examples given in Figure 10.21 (lower left). In conditions when the supply of tryptophan is plentiful, the operon is repressed because the repressor protein Pcorepressor complex is bound at the operator. When tryptophan is in short supply, the corepressor is inactive, therefore has reduced specificity for the operator, and is stored elsewhere on DNA.

Deprivation of repressor causes ~70-fold increase in the frequency of initiation events at the trp promoter. Even under repressing conditions, the structural genes continue to be expressed at a low basal or repressed level. The efficiency of repression at the operator is much lower than in the lac operon (where the basal level is only ~1/1000 of the induced level).

We have treated both induction and repression as phenomena that rely upon allosteric changes induced in regulator proteins by small molecules. Other means also can be used to control the activities of regulator proteins. One example is OxyR, a transcriptional activator of genes induced by hydrogen peroxide. The OxyR protein is directly activated by oxidation, so it provides a sensitive measure of oxidative stress. Another common type of signal is phosphorylation of a regulator protein.