Promoters allow genes to be turned on in groups or at different levels due to their strength. However, genes (operons) have to be turned off and on individually as needed. The structure involved in this process is the operator. A classical operator is located near the promoter and sometimes overlaps it. Proteins bound to the operator must be able to interact with the promoter region so that gene (operon) transcription can be influenced. Operators work by binding proteins which then influence the ability of RNA polymerase to transcribe the gene(s).

When a gene (operon) is turned on only under specific conditions, it is known as a conditional gene (operon).

A gene that is usually turned off by an inhibitor (repressor) and only turned on only when certain substrates (inducer(s)) are present, or when concentration of various metabolites in or outside of the cell reach a certain level is known as an induced or NEGATIVELY REGULATED gene. Turning genes off due to conditions in the cell or growth medium is known as repression and is mediated through repressor proteins. Sometimes other substances are needed (in addition to the repressor), such as the end products of the enzymatic reaction in which the gene (operon) is active. These factors are known as corepressors. Turning on a repressed gene usually requires the action of inducer protein(s) which might be substrates for the action of the gene product(s) or other, unrelated substances. Inducers which are not involved in the enzymatic action of the induced gene (operon) are known as gratuitous inducers.

POSITIVELY REGULATED genes are not repressed, bur are turned on by effector molecules.

A gene (operon) which is always turned on is known as a CONSTITUTIVE gene (operon).

Enhancers are regions of DNA that can be up to 1 kb from the gene (in either direction) which bind proteins and affect gene transcription.

Control of induction or repression

is carried out by a separate regulator gene, which codes for a repressor or inducer protein. Operators are usually under positive or negative regulation.

I. Negative Regulation:

A) Protein(s) binds to operator (enhancer), blocks RNA polymerase from binding, turns off operon.
B) Protein(s) binds to operator (enhancer), destabilizes RNA polymerase binding, turns off operon.
Operon genes are expressed unless regulator protein (repressor) is present; defective or inactivated regulator leads to synthesis of genes under coordinate regulation.

II. Positive regulation:

A) Regulator protein (apoinducer) binds to operator, interacts with RNA polymerase and helps initiate transcription.
B) Other RNA polymerase subunits (s) turn operon on
C) Antiterminators allow operon to be read.
Operon genes are expressed only in the presence of a regulator protein; a defective or inactivated regulator protein turns off genes.

Inducible operons

are on only in the presence of the inducer molecule, which inactivates the repressor.

Repressible operons

only function in the absence of the corepressor molecule (which interacts with the repressor molecule to turn off the operon); active (on) state is derepressed.


Example 1: lac operon:

The substrate for the operon is lactose (a β-glycoside), which acts as an inducer.
There is coordinate regulation of lac Z, Y, and A, which are all regulated by the lac promoter and operator at once.
The lac I gene is a regulator gene (repressor) and is negatively regulated. Mutations which inactivate lac I make the lac operon constitutive.
The lac I gene product (repressor) has 3 types of binding sites.
1) to DNA (operator)
2) to itself (to form tetramers)
3) to inducer - lactose - (changes conformation, can no longer bind operator tightly).
Binding to DNA increases stability.

Inducer binding (probably to core) destabilizes binding, conformation changed, allows RNA polymerase to bind promoter. If remove inducer, tetramer can slide back to operator. Surplus repressor protein is stored in this fashion.

Repression is dominant, constitutive mutants are recessive; inducibility is dominant. Uninducible operator mutants can't be turned on, either RNA polymerase can't bind or repressor can't dissociate.

Example 2: bio operon:

The operon is involved in the linkage of biotin to a specific biotin binding protein (apo-BCCP). Biotin functions as a specific cofactor that carries activated CO2 groups in metabolism. E. coli biotin - protein ligase (33.5kd) "BirA" is the repressor protein that regulates transcription of the biotin operon. It also functions as the enzyme that attaches Biotin-AMP to the acceptor protein, and is a member of the bio operon.

High levels of biotin (and /or low levels of apo-BCCP) block the action of both the promoter of the bio operon and the bio A gene. The BirA-biotinoyl-AMP complex accumulates, binds to the bio operator, and represses transcription from both promoters.

Derepression occurs when the supply of biotin is severely limited. All biotinoyl-AMP is rapidly used up in the biotinylation of the acceptor protein.

The BirA protein contains information for:
1. dimerization
2. DNA binding to operator sequence
3. biotin - protein ligase reaction (ATP binding, biotin binding, biotinoyl-AMP binding, recognition and binding of BCCP).
The BirA protein can only bind to the operator when it has previously bound biotinoyl-AMP to its active site.

Example 3: Anti termination:

The σ subunit leaves the RNA polymerase holoenzyme early in mRNA synthesis. Part of it takes the place of RNA in the open complex, and once the RNA is synthesized in the closed complex, σ becomes easy to remove and is ejected.

The best described system is the NusA system of bacteriophage lambda. NusA (N utilization protein) - 69 kd - binds to the polymerase, forming α2ββ'NusA which can then bind N protein and read through ρ terminators, or it can bind ρ, and terminate. The N protein is unstable, and must be continuously synthesized. There are other systems similar to this.

Example 4: Phosphorylation as a method of control: The Bgl operon

The Bgl operon acts in the uptake and metabolism of beta glucosides such as Salicin and Arbutin. In order to transport the sugar across the cell membrane, it must be phosphorylated and actively transported. It operates in the following manner: In the absence of the beta glucoside substrate (inducer), the BglF gene product, F, will phosphorylate the BglG gene product, G. This inactivates the G protein, and the operon is terminated at one of the twoρ independent terminators. In the presence of inducer, the F protein will change its specificity. It will dephosphorylate G and will phosphorylate the beta glucosides. The beta glucosides will then enter the cell and will be available to be acted on by the other members of the Bgl operon. G will act as an antiterminator, complexing with RNA polymerase and allowing it to read through the terminators, thus transcribing the operon.

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