Table of Contents
Basic principles of transcriptional control in prokaryotes
In prokaryotes, most regulation of gene activity happens at the level of transcription initiation. The central question is: will RNA polymerase bind a promoter and start making RNA, or not?
Three key DNA elements participate:
- Promoter – where RNA polymerase binds and starts transcription.
- Operator – short DNA sequence, usually overlapping or adjacent to the promoter, where regulatory proteins bind.
- Structural genes – protein‑coding genes that are transcribed into a single mRNA (often as an operon).
Regulatory proteins control transcription by recognizing specific operator sequences:
- Repressors bind DNA and inhibit transcription.
- Activators bind DNA and stimulate transcription.
Small molecules (often products or substrates of metabolism) bind these regulatory proteins and change their activity. In this way, the cell couples gene expression directly to its metabolic state.
Operons as units of transcriptional control
An operon is a cluster of genes under the control of a single promoter and operator, transcribed together into one polycistronic mRNA.
Typical structure of a simple operon:
- Regulatory gene (often elsewhere on the chromosome) → encodes a regulatory protein (repressor or activator).
- Promoter (P) → binding site for RNA polymerase.
- Operator (O) → binding site for regulatory protein.
- Structural genes (e.g.
lacZ,lacY,lacA) → encode enzymes or transporters in a pathway.
Because all genes in an operon share one promoter, transcriptional control at that promoter simultaneously regulates the entire set of encoded proteins.
Negative and positive control
Transcription in prokaryotes can be controlled in two basic ways:
- Negative control – a repressor protein binds DNA and blocks transcription.
- Transcription is ON by default but is turned OFF when the repressor is active.
- Positive control – an activator protein binds DNA and helps RNA polymerase initiate transcription.
- Transcription is weak or OFF by default but is turned ON (or strongly increased) when the activator is active.
Small molecules can convert regulatory proteins between active and inactive forms. Two recurring situations:
- Induction – a small molecule (inducer) inactivates a repressor or activates an activator, turning transcription ON.
- Repression – a small molecule (corepressor) activates a repressor or inactivates an activator, turning transcription OFF.
The lac operon as a model for inducible, negatively controlled genes
The lac operon in Escherichia coli controls the use of lactose as a carbon source and is a classic example of transcriptional control.
Genetic components
Key parts:
- Regulatory gene
lacI - Encodes the Lac repressor protein.
- Usually has its own promoter, separate from the operon.
- Promoter
P_lac - Binding site for RNA polymerase.
- Operator
O_lac - Overlaps or is very close to the promoter.
- Binding site for Lac repressor.
- Structural genes
lacZ– encodes β‑galactosidase (breaks lactose into glucose + galactose).lacY– encodes lactose permease (imports lactose).lacA– encodes transacetylase (auxiliary function).
Negative control by the Lac repressor
- In the absence of lactose:
- Lac repressor (product of
lacI) is in its active DNA‑binding form. - It binds the operator and physically prevents RNA polymerase from starting transcription.
- Result: lac operon is essentially OFF; little or no
lacZYAmRNA is produced. - In the presence of lactose:
- A metabolite of lactose (allolactose) acts as an inducer.
- Allolactose binds the Lac repressor and alters its shape.
- The repressor can no longer bind the operator.
- RNA polymerase gains access to the promoter and can transcribe
lacZYA. - Result: lac operon is ON; enzymes for lactose uptake and breakdown are synthesized.
Thus, the lac operon is an inducible operon: normally off, but turned on in the presence of its substrate (lactose).
Positive control of the lac operon by CAP–cAMP
The lac operon is also regulated by a positive control system that responds to glucose availability.
- CAP (catabolite activator protein), also called CRP, is an activator protein.
- cAMP (cyclic AMP) is a small molecule whose concentration increases when glucose is scarce.
Mechanism:
- Low glucose → high cAMP:
- cAMP binds CAP.
- The CAP–cAMP complex binds a specific site near the lac promoter.
- This binding helps RNA polymerase bind the promoter and initiate transcription efficiently.
- If lactose is also present (repressor inactive), lac transcription is high.
- High glucose → low cAMP:
- Little CAP–cAMP complex forms.
- CAP does not bind the promoter.
- Even if lactose is present and the repressor is inactive, RNA polymerase binds less efficiently.
- Lac transcription is low.
As a result, E. coli preferentially uses glucose. The lac operon is strongly expressed only when:
- Lactose is present (repressor OFF), and
- Glucose is low (CAP–cAMP ON).
This combined control illustrates how bacteria integrate multiple environmental signals at the transcriptional level.
The trp operon as a model for repressible, negatively controlled genes
The trp operon in E. coli encodes enzymes for the synthesis of the amino acid tryptophan. It demonstrates another pattern of transcriptional control.
Genetic components
Key parts:
- Regulatory gene
trpR - Encodes the Trp repressor.
- Located some distance away from the operon.
- Promoter
P_trpand operatorO_trp - Operator overlaps the promoter.
- Structural genes
trpE,trpD,trpC,trpB,trpA- Encode enzymes of the tryptophan biosynthetic pathway.
Repression by an end product (corepressor system)
- In the absence of tryptophan:
- Trp repressor is synthesized in an inactive form.
- It does not bind the operator effectively.
- RNA polymerase can bind the promoter and transcribe the operon.
- Enzymes for tryptophan synthesis are produced.
- In the presence of ample tryptophan:
- Tryptophan itself acts as a corepressor.
- It binds the Trp repressor and activates it.
- The activated repressor–tryptophan complex binds to the operator.
- This blocks RNA polymerase, reducing or stopping transcription.
- Enzyme synthesis is decreased when tryptophan is already plentiful.
The trp operon is a repressible operon: normally on, but turned off when its end product (tryptophan) is abundant.
Note: the trp operon is also subject to a finer control mechanism called attenuation, which involves coupling of transcription and translation. Attenuation is a separate layer of regulation beyond basic transcription initiation and is treated elsewhere.
DNA‑binding proteins and recognition of operators
A common feature of transcriptional regulators in prokaryotes is their ability to recognize specific DNA sequences.
Important points:
- Many bacterial regulators are homodimers (two identical subunits).
- Each subunit often contains a helix‑turn‑helix motif, a structural element that fits into the major groove of DNA.
- The protein contacts specific base pairs via hydrogen bonds and other interactions, recognizing a particular operator sequence.
- Operators are often short, palindromic sequences (the two halves read similarly in opposite directions), which match the symmetry of a dimeric protein.
Binding characteristics influence control:
- High‑affinity binding ensures tight repression when the repressor is active.
- Changes in protein shape (induced by binding small molecules like allolactose or tryptophan) alter DNA affinity and thereby regulate transcription.
Global transcriptional control and regulons
Beyond individual operons, bacteria also use transcriptional control to coordinate many genes at once.
A regulon is:
- A set of genes or operons scattered across the chromosome,
- All controlled by the same regulatory protein or signal.
Examples (without detailed mechanisms):
- Genes activated by CAP–cAMP form part of a global catabolite repression regulon.
- Stress responses (such as heat shock) involve alternative sigma factors that recognize distinct promoter sequences and turn on many stress‑response genes as a group.
At the transcriptional level, global control often works by:
- Using common regulatory proteins (like CAP), or
- Switching sigma factors, which redirect RNA polymerase to specific promoter types.
Summary of transcriptional control strategies in prokaryotes
Typical strategies include:
- Negative control with inducers (e.g. lac operon)
- Substrate present → inactivates repressor → operon ON.
- Negative control with corepressors (e.g. trp operon)
- End product abundant → activates repressor → operon OFF.
- Positive control with activators (e.g. CAP–cAMP)
- Signal molecule present → activates activator → transcription stimulated.
- Combination of controls
- Multiple inputs (like lactose and glucose) converge on the same promoter, integrating environmental information.
These mechanisms allow prokaryotes to turn genes on and off rapidly and economically in direct response to nutrient availability and other environmental conditions.