Prokaryote Gene Regulation 2023 2024

Control of gene expression
Dr. Mai Thi Phuong Nga

LS Department
[email protected]
KEY CONCEPT
Gene expression is carefully regulated in both prokaryotic and

eukaryotic cells.
Prokaryotes gene regulation:
• Prokaryote gene expression typically is regulated by an operon

Operon and Prokaryotic Gene Expression
• Operon- A group of prokaryotic genes with a related function

that are often grouped and transcribed together.
• Operon has only one promoter region for the entire operon.
• operon – including structural genes and control elements in

DNA 4
Operon
• regulator – A gene that codes for a product (typically protein)
that controls the expression of other genes at a target site on
DNA.
• (usually at the level of transcription).
• structural gene – A gene that codes for any RNA or protein
product other than a regulator.
Differences between prokaryotes and eukaryotes:
• Eukaryotic genes also are regulated in units of protein-coding sequences

and adjacent controlling sites, but no operons.
• Eukaryotic gene regulation is more complex because eukaryotes possess

a nucleus.
(transcription and translation are not coupled).
• Two “categories” of eukaryotic gene regulation exist:
Short-term - genes are quickly turned on or off in response to the

environment and demands of the cell.
Long-term - genes for development and differentiation.

Regulator Genes and Repressors
• Regulator gene- This gene produces a repressor that can inhibit
the transcription of an operon by attaching to the operator.
9
Interaction of Modulators and Repressors
• Repressors have allosteric properties. Modulators can bind to the

repressor at an allosteric site changing the conformation of the
repressor, thereby activating or deactivating the repressor.
• Usually the modulator is a product of the biochemical pathway.
10
Type of regulation
• In negative regulation, a repressor protein binds to

an operator to prevent a gene from being expressed.
• In positive regulation, a transcription factor is

required to bind at the promoter in order to enable
RNA polymerase to initiate transcription.
Operon
In positive control, a trans-acting activator

In negative control, a trans-acting must bind to cis-acting site in order for RNA
repressor binds to the cis-acting operator polymerase to initiate transcription at the
to turn off transcription. promoter.
Many bacterial genes are transcribed and
regulated together in an operon
Genes are transcribed together
First example: the lac operon

The lac Operon Reveals Many
Principles of Gene Regulation
• Work of Jacob and Monod − 1960

• Shows how three genes for metabolism of lactose are
regulated together as an operon:
o -galactosidase (lacZ)
• cleaves lactose to yield glucose and galactose
o lactose permease (galactoside permease; lacY)
• transports lactose into cell
o thiogalactoside transacetylase (lacA)
• They rely on negative regulation via a repressor.

Lactose Metabolism in E. Coli
 Uptake and metabolism of lactose require the

activities of galactoside permease and β-
galactosidase.
 Conversion of lactose to allolactose by

transglycosylation is a minor reaction also
catalyzed by β-galactosidase.
Lactose Metabolism in E. Coli
• When glucose is abundant and lactose is lacking,
cells make only very low levels of enzymes for
lactose metabolism.
o Transcription is repressed.
• If glucose is scarce and cells are fed lactose

The cells suddenly express the genes for the
enzymes for lactose metabolism.
o Transcription is no longer repressed.
Structure of the lac Operon
The Lac repressor binds primarily to the operator O1.
Binding of the repressor helps prevent RNA polymerase from

binding to the promoter.
Inhibiting the Transcription of the lac
Operon via a Repressor Protein
• A gene called lacI encodes a repressor called

the Lac repressor.
o The repressor can bind to three operator sites
(O1–O3).
Lac Repressor Bound to O1 and O3
with DNA Looped Between
The repressor also binds to one of two secondary operators, with

the DNA looped between this secondary operator and O1
The lac Operon Is Induced by
Allolactose
• Allolactose (an inducer) binds to the repressor and
causes it to dissociate from the operator.
o -galactosidase can also isomerize lactose into
allolactose.
– [Allolactose]  when [Lactose] 

How Lac Repressor Binds to DNA
• Lac repressor is a tetramer.
• The O1 sequence reflects the symmetry of the repressor.
• There are approximately 20 repressors per cell.

The lac Operon Is Governed by More
Than Repressor Binding
• The availability of glucose governs expression of lactose-

digesting genes via catabolite repression.
o When glucose is present, lactose genes are turned off.
o It is mediated by cAMP and cAMP receptor protein (CRP

or CAP for catabolite activator protein).
When Glucose Is Absent, lac Operon
Transcription Is Stimulated by CRP-cAMP
• cAMP binds near the
promoter.
o stimulates transcription 50-
fold
• cAMP is made when

[glucose] is low.
• CRP-cAMP only has this

effect when the Lac
repressor has dissociated.
When Lactose Is Absent
Little to No Transcription Occurs
Whether [glucose] is high or low, if lactose is absent  repressor
stays bound…. no transcription even when CRP-cAMP bind.
When lactose is absent, the repressor binds to the operator and prevents transcription of
the lac genes. It does not matter whether glucose is (a) present or (b) absent.
When Lactose Is Present, Transcription
Depends On Glucose Level
• Repressor dissociates, but transcription is only stimulated
significantly if cAzMP rises.
 If lactose is present, the repressor dissociates from the operator. However, if glucose is also
available, low cAMP levels prevent CRP-cAMP formation and DNA binding. RNA
polymerase may occasionally bind and initiate transcription, resulting in a very low level of
lac gene transcription.
 When lactose is present and glucose levels are low, cAMP levels rise. The CRP-cAMP
complex forms and facilitates robust binding of RNA polymerase to the lac promoter and
high levels of transcription.
Two Requirements for Strongest
Induction of the lac Operon
1. Lactose must be present to form allolactose to bind to
the repressor and cause it to dissociate from the operator.
• causing activation
2. [Glucose] must be low so that cAMP can increase, bind

to CRP, and the complex can bind near the promoter
• causing activation
Combined Effects of Glucose and
Lactose on the lac Operon
• When lactose is low, repressor is bound: inhibition

• When lactose is high, repressor dissociates
permitting transcription
• When glucose is high, CRP is not bound and
transcription is dampened
• When glucose is low, cAMP is high and CRP is
bound activation

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Control of gene expression

Dr. Mai Thi Phuong Nga

Gene expression is carefully regulated in both prokaryotic and

• Prokaryote gene expression typically is regulated by an operon

• Operon- A group of prokaryotic genes with a related function

• operon – including structural genes and control elements in

• Eukaryotic genes also are regulated in units of protein-coding sequences

• Eukaryotic gene regulation is more complex because eukaryotes possess

(transcription and translation are not coupled).

• Two “categories” of eukaryotic gene regulation exist:

Short-term - genes are quickly turned on or off in response to the

Long-term - genes for development and differentiation.

• Repressors have allosteric properties. Modulators can bind to the

• Usually the modulator is a product of the biochemical pathway.

• In negative regulation, a repressor protein binds to

• In positive regulation, a transcription factor is

In positive control, a trans-acting activator

Genes are transcribed together

First example: the lac operon

• Work of Jacob and Monod − 1960

• They rely on negative regulation via a repressor.

 Uptake and metabolism of lactose require the

 Conversion of lactose to allolactose by

• If glucose is scarce and cells are fed lactose

The Lac repressor binds primarily to the operator O1.

Binding of the repressor helps prevent RNA polymerase from

• A gene called lacI encodes a repressor called

The repressor also binds to one of two secondary operators, with

– [Allolactose]  when [Lactose] 

• The O1 sequence reflects the symmetry of the repressor.

• There are approximately 20 repressors per cell.

• The availability of glucose governs expression of lactose-

o When glucose is present, lactose genes are turned off.

o It is mediated by cAMP and cAMP receptor protein (CRP

• cAMP is made when

• CRP-cAMP only has this

2. [Glucose] must be low so that cAMP can increase, bind

• When lactose is low, repressor is bound: inhibition

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