REGULATION OF GENE

EXPRESSION IN
PROKARYOTES AND
EUKARYOTES
Presenter : Dr. KUSH GABA
DEPARTMENT OF BIOCHEMISTRY

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 GENE REGULATION AND EXPRESSION
Gene regulation is defined as ability of an organism to control or
regulate what proteins makes its from DNA

Synthesis of proteins, under the influence of gene is called Gene

expression.
For development ,differentiation, and adaptation regulated
expression is required
Expression of gene products depend on their utility & amount
required at a given time.
All genes of the cell are not expressed always.
 TYPES OF GENE

OR
Non housekeeping
genes.
 HOUSEKEEPING GENES

• Genes which are expressed all the time at a relatively constant rate
called housekeeping genes.
• Eg. Enzymes of glycolysis

• Their continuous expression is called constitutive expression.

 NON- HOUSEKEEPING GENES
• The genes which are transcribed only when needed are called non
housekeeping genes.

• These genes are also called regulated gene.

• Expression of this genes are regulated by the presence or absence of

specific metabolites called Inducers or Repressors.
 WHY REGULATION OF GENE
EXPRESSION IS NEEDED?
It is expensive
( to save such huge amounts of energy)
To adapt to changing environmental condition
For the alteration of conc. of metabolic enzymes

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TYPES OF RESPONSES TO REGULATORY SIGNAL
 Different types of cellular response to regulatory signal
X AXIS – GENE EXPRESSION
Y AXIS- TIME
TYPE C (SUSTAINED
RESPONSE)The response is
initially low, but once the
signal is introduced, it
increases and remains high,
even if the signal stops.
Eg: immune response

TYPE B (TRANSIENT
TYPE A RESPONSE)The response
ON AND OFF RESPONSE peaks sharply after the signal
The response follows the signal is introduced but then
input almost exactly, turning on quickly declines, even if the
and off as the signal appears and signal persists.
disappears. Eg: hormone Eg:feed back mechanism
regulated gene expression
 INDUCTION
Induction-turning ‘on’ the switch of the gene

⮚ Induction is the process by which gene expression is regulated

positively by a specific regulatory signal.
⮚ Signal may be a low molecular weight molecule called Inducer.
⮚ Genes whose expression is increased in response to inducers
are called Inducible genes.
 REPRESSION
Repression -turning ‘off’ the switch of the gene

❑ Repression is the process by which gene expression is regulated

negatively by the presence of repressor molecules.
❑ During repression the genes are not expressed.

❑ Removal of the repressor molecule, genes are again expressed.

Process is called derepression.
FACTORS AFFECTING GENE REGULATION
• PROMOTERS & THEIR VARIATION

• CIS ACTING DNA ELEMENT & TRANS ACTING REGULATORY PROTEINS

THEIR INTERACTIONS

• PROTEIN BINDING DOMAINS IN REGULATORY PROTEINS

• PROMOTERS & THEIR VARIATION

• Promoters are specific sequences in DNA, where RNA polymerase

binds for initiation of transcription

• Variation in promoter sequences affects the affinity of RNA

polymerase to the promoters
• Shift away from consensus(Identical DNA sequence found in
promoter region) : decreased promoter function

• Shift towards consensus : increased promoter function

CIS ACTING DNA ELEMENT & TRANS ACTING REGULATORY PROTEINS

• Trans-acting regulatory proteins are

CIS-acting DNA elements are proteins that bind to specific DNA
specific binding sites DNA sequences (CIS-acting elements) or
sequences in regulatory proteins. other proteins to regulate gene
These elements regulate gene expression, often acting at a
expression by interacting with distance from the genes they
trans-acting regulatory proteins. control.
Examples: Promoters (e.g., TATA • These proteins can either activate or
box repress gene expression
• Examples: - Transcription factors
(e.g., TBP, )
 CIS ACTING DNA ELEMENT & TRANS ACTING
REGULATORY PROTEINS

 Cis-acting DNA Trans-acting regulatory proteins

encoded by different genes on
elements are regulatory different chromosomes) that
sequences located on regulate target genes.
the same DNA the gene Here Transcription factors (TFs)
they regulate. that are produced elsewhere
 Examples: Promoters, but bind to promoter/enhancer
enhancers regions of the gene.
 Here enhancers and TFs being transcribed from one
promoters interacting gene and then acting on
another gene's enhancer or
with transcription
promoter region to regulate
factors (TFs) to regulate expression.
the adjacent gene.
 PROTEIN BINDING DOMAINS IN
REGULATORY PROTEINS
• Regulatory proteins contain domains
• This interaction Between which leads to protein-protein
cis-acting & trans-acting interactions
proteins regulate a target • These Protein binding domains also
gene in either a Positive contain some Structural Motifs that
Manner or a Negative Mediate the Interaction.
Manner.
• Leucine Zipper : Mainly, in Eukaryotic
& Some Bacterial Proteins
• Basic Helix-Loop-Helix : In some
Eukaryotic Regulatory Proteins
PROKARYOTIC GENE REGULATION
• There are defined mechanisms that can increase or decrease
expression of gene as per the requirement of the cell at different
stages.

• In prokaryotes most of regulation is at in transcription initiation step

(that before RNA polymerase begins transcription) mainly in
isomerization step once RNA polymerase move from close complex to
open complex),
• And also post initiation transcription and post translation also .

• There are two types of regulators positive regulator /activators and

negative regulator /repressor.
GENE REGULATION
 PRINCIPLES OF TRANSCRIPTIONAL
REGULATION
These genes are expressed in
the cell all times
E This promotor
G EN bind to RNA
F
ESO polymerase
P
TY Initiation can start
TW
O DNA any times.

RNA
This promotor
bind to activators In prokaryotes
or repressor and Control points start
influence the from transcription
expression of
gene
REGULATION OF GENE EXPRESSION-PROKARYOTES EXPLAINED BY
OPERON CONCEPT

In prokaryotes a group of genes organised into a functional unit with a single

promoter control present in a linear array called an operon.
Include structural genes, regulator/ inhibitor gene, promoter and operator
areas.
■ Eg : lac operon
Lac : lactose ,(disaccharide sugar present in milk)
Operon: group
Group of gene which regulate the metabolism of lactose
LACTOSE METABOLISM IN [Link]
 Lac operon can be
divided into 2 important
regions
Structural genes
Regulatory genes
TERMINATOR
Structural genes code for
enzyme.
Regulatorygenes:controle
these structural gene.

Regulatory region allow

the bacteia to “switch on”
or “ swicth off” structural
gene if if lactose is
present or not
 LAC OPERON
Lac operon comprises of
3 Structural genes
Lac Z ,Lac Y ,Lac A

⮚ Lac Z – Beta
galactosidase,an enzyme
in [Link] which hydrolyses
beta glycosidic linkage of
Lactose.
⮚ Lac Y – code for protein Beta
galactoside Permease- a tube
like carrier protein that fix in
the bacteria helps permeation
of more lactose into the cell.

⮚ Lac A – Beta
galactosideTransacetylase- An
enzyme that transfer acetyl
group from acetyl coA to Beta
galactoside (function is not
fully understood)
 LAC OPERON - REGULATOR REGION
Promoter region :Located upstream of the structural genes,binding site
of RNAP.
Operator region
Lac I gene – code for protein repressor

AT THE END HAVE TERMINATOR

[Link]- normal resident bacteria present in our gut .it eats what
we eat.
Most of the time it eats carbohydrate containing food which can
easily broken down in gut
 Glucose is the preferred Energy Source for E. Coli as it is metabolized
only through Glycolysis

 Metabolism of Lactose, require Additional three Enzymes ~ Synthesized

only when :
 Lactose is Present &
 Glucose is Absent
• RNA POLYMERASE COPY THE INFORMATION OF 3 STRUCTURAL
GENE OF LAC OPERON TO mRNA

LAC OPERON- OFF

• RNA polymerase always bind to a site just behind structure gene

called promotor
• Infront of promotor we have operator which can “switch on” or “
swicth off”
• When it off RNA polymerase cannot move forward on DNA ,genes
cannot transcribe.
• lac i gene (i-inducable) ,these gene
continously synthesis a protein
called REPRESSOR
• REPRESSOR-attaches operator –
then it is called bound state of
repressor –then operator become “
TURN OFF”
• RNA polymerase cannot move
forward on DNA.
 LAC OPERON- ON
• LACTOSE PRESENT IN THE MILK WHICH MAKE SWTICH ON LAC OPERON

• Repressor changes its configuration when ever it get (milk sugar)

• Repressor is in bound state with operator which prevent RNA

polymerase .
• Repressor has a site which recognize lactose and fit this site
• When lactose bind this site Repressor changes its configuration, and
operator become free. “switch on” operator
• RNA polymerase move forward on DNA , transcription occur.
 Lac operon a group of genes located on DNA OF bacteria E Coli
Utilize lactose
2 condition should be there to activate lac operon
Lactose is Present- (changes the structure of repressor
SUMMARY OF protein to release from operator site)
Glucose is Absent –(activate another protein CAP ,Allow the
REGULATION RNA polymerase binding to promotor site and transcription
OF LAC OPERON occur)
 TRYPTOPHAN OPERON
Contains 5 structural genes
needed to produce the enzymes
involved in tryptophan synthesis

When Trp concentration is

high,Trp binds to repressor
protein,binds to operator site

At low concentrations,the
repressor is not bound to
operator…..gene transcription
occurs.
Operator (O): trp
repressor binds when
activated. Binding of the
repressor blocks RNA
polymerase, preventing
transcription

trpR (Regulatory
Gene):Produces the trp
repressor protein, Leader & Attenuator
which regulates the Sequences:Leader sequence:
operon Contains codons that sense
tryptophan levels
Promoter (P):The binding
Attenuator sequence:
site for RNA polymerase, Regulates transcription
which initiates termination based on
transcription of structural tryptophan availability
genes.
CONT..
• When Tryptophan Levels Are High (Repression Occurs)
• Tryptophan acts as a corepressor by binding to the trp repressor protein, activating
it.
• The activated repressor binds to the operator (O), blocking RNA polymerase.
• No transcription → No enzyme production → Tryptophan synthesis stops.

• When Tryptophan Levels Are Low (Operon Active)

• The trp repressor remains inactive because no tryptophan is available to bind
• RNA polymerase binds to the promoter (P) and transcribes structural genes.
• Enzymes for tryptophan synthesis are produced.
• Attenuation Mechanism (Fine-Tuning Control)(If tryptophan is partially available), the
operon uses attenuation (premature transcription termination).
• A hairpin loop forms in mRNA, causing early termination when tryptophan is
sufficient.
• If tryptophan is scarce, the ribosome stalls, and transcription continues
REGULATION OF HEME SYNTHESIS
■ Regulatory gene produces apo-
repressor, which binds with
heme(corepressor) and become
holorepressor.
■ Holorepressor binds to operator
and stops transcription of gene.

■ When heme is not available,

corepressor is not available
repression is not effective, enzyme
synthesis starts.
 REPRESSION-ALA SYNTHASE

Regulator Promoter Operator Structural gene

DNA RNAP ALA Synthase

mRNA mRNA
Holo repressor
ALA Synthase

Aporepressor
Co repressor- Heme
REGULATION OF GENE EXPRESSION
EUKARYOTES
• REGULATION OF GENE • GENE EXPRESSION IN
EXPRESSION MORE COMPLEX IN EUKARYOTES IS THE COMBINED
EUKARYOTES PROCESS OF
[Link] genome is significantly larger
■ The transcription of a gene
2. Different cell types into mRNA.
3. Absence of operons ■ The processing of that mRNA.
4. Chromatin structure ■ Its translation into protein
Transcription ,translation processes (for protein-encoding genes
 REGULATION IN EUKARYOTES
1. Changes in gene level

2. Regulation at the level of transcription

3. Regulation at post transcriptional level

4. Regulation at translational level

(I)CHANGES IN GENE LEVEL

 Gene Amplification
 Gene rearrangement
 Gene Loss
 Gene switching
 Modifications of DNA
GENE AMPLIFICATION
The gene product can be increased by
increasing the number of genes available for
transcription of specific molecules
■ Generated by a process of repeated
initiations during DNA synthesis-provide
multiple sites for gene transcription.
 GENE AMPLIFICATION

■ EXAMPLE :Patients receiving methotrexate for cancer.(It inhibit

dihydrofolate reductase)
■ The malignant cells become resistant to methotrexate by increasing the
number of genes for dihydrofolate reductase, produce excess target
protein ( more enzyme).making drug less effective.
GENE REARRANGEMENT
 GENE REARRANGEMENT
■ The heavy chain consists of a variable region
(VH) and a constant region (CH).
• A segment from the DNA moves from one
location to another on the genome.
• This forms new combination of genes so ■ The complete VH gene (the functional form)
that several different proteins are encoded
is formed by assembly of three different
• DNA segments are brought together and
types of genes: the variable gene, V; the
combined to produce the active gene.
• Eg: immunoglobulin synthesis. diversity gene, D; and the joining gene, J.
 GENE LOSS GENE SWITCHING

■ Certain genes may be lost from a ■ It is a phenomenon in which transcription and

translation of a given gene stops, and
cell so that the functional protein expression of a related gene is turned on.
encoded by them are not
produced. ■ In immunoglobulins,Ig M is the formed during
primary immune response, while Ig G is
 During differentiation of red blood
formed during secondary immune response.
cells, the nuclei are extruded
■ Thus, switching of genes from IgM to IgG
resulting in complete loss of all
occurs.
genes.
GENE SWITCHING (Eg: Hb synthesis)
• During intrauterine life embryonic Hb
is the first Hb to be formed-two “Zeta”
and two “Epsilon” chains.
• By the sixth month of intrauterine life,
embryonic Hb is replaced by HbF
consisting of “α2 and γ2 chains.
• After birth HbF is replaced by adult
type of 97% Hb A1 (2α & 2 β) and 3%
HbA2 (2α & 2δ)
• Thus the genes for a particular class of
Hb are switched off and for another
class are switched on.
 MODIFICATIONS OF DNA

■ The highly methylated areas

of DNA are transcriptionally ■ More the methylation, less is
inactive-Methylation leads to the frequency of
silencing of the gene
transcription
■ Methylated DNA prevent the
binding of transcription
factors
(II)REGULATION AT LEVEL OF TRANSCRIPTION

Chromatin Remodelling
 Enhancers & repressors
 CHROMATIN
REMODELLING
■ Large regions of chromatin are transcriptionally inactive or
either active or potentially active in other specialized cells

■ "Active" chromatin

■ "inactive" chromatin
CHROMATIN REMODELLING

• HISTONE ACETYLATION AND DEACETYLATION

• MODIFICATION OF DNA-METHYLATION
• DNA BINDING PROTEINS
• HISTONE ACETYLATION AND
DEACETYLATION
• MODIFICATION OF DNA-METHYLATION
• This will reduces the positive charge
■ Methylation of deoxycytidine
of tails and decreases the binding
residues in DNA may effect gross
affinity of histone for the negatively
changes in chromatin -inhibits
charged DNA.
transcription
• Disruption of nucleosomal structure

• Allows the access of transcription

factors to the regulatory DNA
elements
• DNA BINDING PROTEINS
■ Many eukaryotic genes have multiple protein-binding DNA elements or

sequences called response elements.

Binding of transcription factors to these elements directly disrupt the structure

of the nucleosome…increase DNA accessibility to other factors.

ENHANCERS & REPRESSORS
ENHANCERS
■ Enhancer elements are DNA sequences, although
they have no promoter activity of their own but they
greatly increase the activities of many promoters in
eukaryotes.
■ Enhancers function by serving as binding sites for
specific regulatory proteins.
• HORMONE RESPONSE ELEMENTS (HRE)
■ hormones act as second messengers function as
inducers.
■ Elicit physiological response through controlling
gene expression
 Action of steroid
hormones
■ Glucocorticoids attach
to a cytoplasmic Hormone
receptor; then the
receptor-hormone
complex translocate to
the nucleus attaches
on the HRE in the
DNA. Enhancer
Promoter
■ The receptor binds at
HRE
the enhancer region,
which activates the H-R Complex mRNA
promoter, so that
transcription is
accelerated
Repressors or silencers

■ The elements that decrease the expression of specific genes

■ may be located thousands of base pairs away from the gene

they control

■ when transcription factors bind to them, expression of the

gene they control is repressed

■ Eg: GAL1: A gene involved in galactose metabolism

(III)REGULATION AT POST TRANSCRIPTIONAL
LEVEL
■ There is Alternative RNA processing for control gene
expression in eukaryotic cells.
■ This can result when alternative promoters, intron-exon
splice sites, or polyadenylation sites are used.
■ The same primary transcript is processed differently in
different tissues
A) ALTERNATIVE PROMOTERS

■ alternative promoters in different tissues produce

transcripts differing in the 5’ portion and the translated
polypeptides differing in the N-terminal sequence
(B) ALTERNATIVE POLYADENYLATION
■ Alternative polyadenylation sites produces transcripts with
different 3’ ends.
 C) TISSUE-SPECIFIC SPLICING
■ If sequences treated as introns by some cells are treated as
exons by others, leads to formation of different mRNAs and
different proteins from a single gene
■ (D) mRNA Editing
enzyme-mediated alteration of RNA in the cell nucleus before
translation
involves insertion, deletion or substitution of nucleotides in the
RNA molecule
(D) mRNA Editing
■ Gene for apo B protein
encodes a mRNA
transcript in the liver and
form a 4536 amino acid
protein apo B100.
■ In the small intestine,
enzyme- catalysed
deamination of a specific
cytidine residue in the
mRNA of apolipoprotein
b-100, by changing
cytidine to uracil, changes
a codon for glutamine
(CAA) to a stop codon
(UAA) in the intestinal
mRNA-apo B 48
 (IV)REGULATION AT TRANSLATIONAL LEVEL

■ Refers to the number of times a finished mRNA molecule is

translated
■ Eg:In conditions of iron excess there is an increase in the
synthesis of ferritin,
■ Deficiency there is a decrease in the synthesis of ferritin and
increase in the synthesis of the transferrin receptor protein
■ The mRNAs for both ferritin and
transferrin receptor contain a
specific sequence known as the
iron-response element (IRE), to
which a specific IRE-binding
protein can bind.
■ When iron is deficient the IRE-
binding protein binds the ferritin
mRNA and prevents translation of
ferritin. It also binds the
transferrin receptor mRNA and
prevents its degradation.
■ Thus in iron deficiency, ferritin
concentrations falls low and
transferrin receptor concentration
rises
■ Reverse occurs in iron excess
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