Regulation of Gene Expression: Proteins must be generated at the correct time for a

cell to operate effectively from information encoded in their DNA, all cells control or
regulate protein production. Regulation of Gene expression is the process of turning on a
gene to produce RNA and protein. Each cell, whether in a basic unicellular organism or a
complex multicellular organism, regulates the frequency and manner its genes are
expressed.

For this to happen, a mechanism must be in place to regulate when a gene is expressed to
produce RNA and protein, how much of the protein is produced, and when the protein is
no longer required. Regulation of gene expression, also known as gene regulation,
refers to the various strategies that cells use to promote or reduce the output of specific
gene products (protein or RNA). Let’s take a closer look at the regulation of gene
expression.

What are Genes?

A gene is a section of DNA that codes for the production of a certain protein. The
information database of the cell is DNA, which is found in the nucleus. It contains all of
the necessary genetic instructions for producing the proteins that our cells require.

Each gene has its own set of instructions, which are usually in a coded format and are
used to perform a certain function or produce a protein.

Fig: Genes

The genes, as mentioned above, are translated into mRNA before being transformed into
a polypeptide chain. After that, a polypeptide is transformed into a protein. Gene
expression is the result of all the hidden coding inside our genes expressing themselves
as physical characteristics.
 Gene Expression
It is a process in which the genetic codes of genes are used to control protein synthesis,
which is necessary for our bodies to form cell structures. Structural genes are genes that
carry information that is needed for amino acid sequencing.

Fig: Gene Expression

There are two main steps in this procedure:

1. Transcription– The messenger RNA is created in this stage with the help of RNA
polymerase enzymes, resulting in the processing of mRNA molecules.
2. Translation– The primary purpose of mRNA is to direct protein synthesis, which leads
to post-translational processing of the protein molecules.

Regulation of Gene Expression at Various Levels

Fig: Gene Regulation

 The cell’s use of a number of procedures to either boost or reduce the production of a
certain gene product is referred to as the regulation of gene expression (a protein or an
RNA). In eukaryotes, the regulation could be exerted at, as explained below.

1. Replication level – Gene expression may be affected by mutations that occur during
DNA replication.
2. Transcriptional level – The Repressors and activators can influence the transcription of
a specific gene.
3. Post-transcriptional level – Post-transcriptional changes, such as RNA splicing, can
result in gene expression.
4. Translational level – RNA interference mechanism, for example, can influence the
translation of an mRNA molecule.
With the help of translation and transcription, gene’s genetic codes are used in managing
the protein synthesis that is required for our body to produce the cell structures.
Information is transferred from genes to proteins in this process.

Let’s use the Keratin genes as an example to comprehend this topic better. Keratin is a
protein that has a role in developing our hair, nails, and skin. In most situations, these
things continue to develop constantly while our hair, nails, and skin wear down over
time. Excessive keratin production can result in a lot of hair on the skin, dry and hard
skin, and thick and long nails. To avoid this, the expression of the keratin gene must be
regulated.

Regulation of gene expression refers to the several processes by which our cells control
the amount of protein produced by our genes.

Regulation of Gene Expression in Prokaryotes and Eukaryotes

Regulation of genes differs depending on whether the organism is prokaryotic or
eukaryotic. Eukaryotes are multicellular and unicellular organisms with nuclei and other
organelles within their cells, such as mammals, fungi, plants, and protists. Prokaryotes
are single-celled organisms without a nucleus, such as bacteria. Because eukaryotes have
a nucleus and prokaryotes do not, prokaryotic and eukaryotic transcription regulation is
fundamentally different.
 Fig: Regulation of Gene Expression in Prokaryotes and Eukaryotes

In the cytoplasm of prokaryotes, transcription and translation occur simultaneously, and

transcriptional regulation occurs. Eukaryotic gene expression is regulated in two ways:
in the nucleus during transcription and RNA processing and in the cytoplasm during
protein translation. Protein post-translational changes may be used to regulate the
process further.

Prokaryotic Transcription Eukaryotic Transcription

It occurs in the cytoplasm. It occurs within the nucleus.
The transcriptional unit has one or more
The transcriptional unit has just one gene
genes
Transcription takes place in the nucleus, while translation takes
Transcription and translation are coupled
place in the cytoplasm.
In the cytoplasm, RNAs are released and
The nucleus processes RNA before releasing it into the cytoplasm.
processed.

How do Cells choose which Genes to Activate or ”Turn on”?

Gene regulation refers to how a cell manages the multiple genes in its genome that are
activated (expressed) or “Turned On.” Even though practically all of the body’s cells
carry the same DNA, gene regulation allows each cell type to have a unique collection of
activated genes. Numerous cell types have diverse sets of proteins due to these different
gene expression patterns, making each cell type uniquely specialised to fulfill its task.

A microbial cell’s DNA contains hundreds to thousands of genes that do not all express
at the same time. Only a few genes express and synthesise the necessary protein at any
given moment. The other genes are currently silent and will express when needed. The
environment in which they grow determines the amount of gene expression required.
This demonstrates that genes have the ability to turn on and off. The genetic code states
that proteins are made up of 20 distinct amino acids. Codons are responsible for the
 production of all proteins. As a result, all amino acid synthesis requires energy, which is
inefficient because all of the amino acids that make up proteins are not required at the
same time.

Different cell types express distinct sets of genes. However, depending on their
surroundings and internal state, two separate cells of the same kind may have diverse
gene expression patterns. In general, we may say that information from both within and
outside the cell influences the gene expression pattern.

What Role do these Cues Play in a Cell’s Decision to Express Certain Genes?
Cells have molecular pathways that transform information into a change in gene
expression, such as binding a chemical signal to its receptor. Consider how cells react to
growth factors as an example.

Fig: Growth Factor Promoting Cell Division

1. The physical binding of the growth factor to a receptor protein on the cell surface allows
it to recognise it.
2. When the growth factor binds to the receptor, it causes it to alter the shape, which sets
off a chain of chemical reactions in the cell that activate transcription factors.
3. The transcription factors attach to certain DNA sequences in the nucleus and induce
transcription of cell division-related genes.
4. These genes produce various proteins that cause the cell to divide (drive cell growth and
proceed through the cell cycle).
It is only one example of how a cell can adjust gene expression in response to a source of
information.
The activation of several targets, including transcription factors and non-transcription
factor proteins, is involved in growth factor signalling.

Regulation of Gene Expression in Prokaryotes:

Prokaryotes’ DNA is structured into a circular chromosome that sits in the cytoplasm of the cell.
Proteins required for a given function or part of the same metabolic pathway are frequently
encoded in operons.

Lac-operon is a system that involves the regulation of protein

synthesis or the synthesis of enzymes by a set of genes. This concept
can be well studied by the gene expression in prokaryotes
like E.coli and other bacteria (Archaea). The concept of Lac-operon
was first explained by Jacob and Monad in E.coli.
Lac-operon refers to the system that can regulate the metabolism or
utilization of lactose (as the sole carbon source). In E.coli, a lac-
operon contains a gene sequence that controls the gene
expression by switching on and switching off the system.
Lac repressor and catabolite activator protein (CAT) are the two gene
proteins in which the former functions as a lactose sensor and the
latter acts as a glucose sensor. Therefore, the lac-repressor and CAT
are the two main components of the Lac-operon.

Lac repressor generally blocks the gene transcription but expresses

itself in the presence of inducer molecules, i.e. lactose. CAT activates
the gene transcription only at low glucose levels through the hunger-
sensing molecule, i.e. cAMP (cyclic adenosine monophosphate). In
this context, we will briefly study the concept, structure, components
and regulation of the Lac-operon system.
Content: Lac-Operon

1. Operon
2. Components of Lac-Operon
 Regulatory Elements
 Structural Elements
3. Video
4. Control of Gene Expression in Prokaryotes
 Positive Control of Lac-Operon
 Negative Control of Lac-Operon
5. Inducer
Operon
It is a system of DNA containing a sequence of genetic codes or
carries a sequence of genes that code the m-RNA and direct the
synthesis of enzymes for protein synthesis. An operon is
a coordinated system in which all the genes coordinate to mediate
the regulation of gene expression.
Components of Lac-Operon
An operon primarily consists of two elements or genes:

Regulatory Elements

It includes the following regions:

 Promotor Region: It codes the Lac-P gene. It lies between the

regulator and the operator. RNA-polymerase binds to this site as a
promoter region initiates transcription. It is 100 base pairs long. It
consists of palindromic sequences. This site promotes and controls
the transcription of structural genes or m-RNA. The regulatory
genes of the repressor regulate the functioning of the promoter
region.
 Operator Region: It codes the Lac-O gene. It lies between a
promoter and the structural gene (Lac-Z). It contains an operator
switch, which decides whether transcription should take place or
not. The regulatory gene binds to the operator.
 Regulator Region: It codes for the regulator gene (Lac-I) that
controls the activity of the promotor and an operator gene. This
regulatory gene produces regulatory proteins known as
“Repressor proteins” that can bind to the promoter and operator.
Structural Elements

These are the regions of DNA, which contain genes for protein
synthesis, and they are of three kinds:

 Lac-Z: Encodes for the enzyme beta-galactosidase.

Function: Beta-galactosidase brings about the hydrolysis of lactose
into galactose and glucose subunits.
 Lac-Y: Encodes for the enzyme lactose permease.
Function: Lactose permease brings lactose into the cell.
 Lac-A: Encodes for the enzyme thiogalactoside transacetylase.
Function: Thiogalactoside transacetylase function is not very clear,
but it assists the activity of the enzyme beta-galactosidase.
These three, i.e. Lac Z, Y and A genes, are present adjacent to each
other. Therefore, all the elements like promotor, operator, repressor
and structural genes together form a unit called Operon.

Control of Gene Expression in Prokaryotes

In prokaryotes, the Lac-operon system is controlled in two ways:

 Positive control
 Negative control
Positive Control of Lac-Operon

It is also called a Positive inducible system and includes the

following steps:
1. Firstly, a regulatory gene expresses the repressor protein.
2. After that, repressor proteins are produced by the expression of a
regulatory gene.
3. A repressor protein has binding sites for the operator and the
inducer (lactose).
4. When lactose is present as an inducer, it binds with the repressor
protein and forms the R+I complex.
5. After the binding of the inducer to the repressor, the complex
blocks the binding of the repressor to the operator.
6. As the repressor protein does not block the operator, the RNA
polymerase binds to the promotor and moves further to transcribed
mRNA.
This concept is known as the switch on of Lac-operon (by the
presence of an inducer).
Negative Control of Lac-Operon

It is also called Negative control of the repressor system. It

includes the following steps:
1. First, the regulatory gene is expressed by the repressor.
2. A repressor protein is produced after the expression of a regulatory
gene.
3. In the absence of an inducer or lactose, the repressor protein
directly binds to an operator.
4. This blocks the movement of RNA polymerase and its attachment
to the promoter.
5. At last, mRNA transcription will not occur.
This concept is known as the switch off of Lac-operon (by the
absence of an inducer).

Inducer

It is also termed an Antirepressor. It suppresses the activity and

binding of the repressor protein to the operator and makes it an
inactive repressor from the active repressor. A lactose or allolactose
functions as an inducer in Lac-operon. Allolactose forms by the
enzyme beta-galactosidase as a result of the isomerization of lactose,
i.e. galactose links to the C6 instead of C4. It is a kind of
complementary substance that participates in switching on and off the
operon system.

Tryptophan operon is found within the genome of E.coli, which

carries a set of genes constructing an essential amino
acid, tryptophan. Sometimes, it is also termed as trp operon. Unlike
lactose or lac operon, trp operon is a repressible system discussed
in this article.
A scientist named Charles Yanofsky and his co-workers explicitly
studied the role of regulatory and structural genes of the trp operon.
Trp operon aids biosynthesis of the amino acid tryptophan from a
precursor molecule (chorismic acid). Tryptophan functions as
an effector molecule that is required for building up the polypeptide
chain.
The tryptophan is the end product of the biosynthetic pathway,
whose combination or dissociation with the repressor protein can turn
on or turn off the trp operon system. This post mainly describes the
definition, structure and regulatory system of the tryptophan operon.
Content: Tryptophan Operon

1. Definition
2. Structure
3. Regulation
 Repression
 Derepression
 Attenuation
Definition

Trp operon is a repressible system that regulates gene expression for

tryptophan biosynthesis according to the binding or uncoupling of a
repressor with the operator region. The association or dissociation of
the repressor protein strongly depends upon the tryptophan level in
the surrounding.
A high level of tryptophan or effector molecule escalates the binding
affinity of a repressor protein with the operator sequence, which in
turn terminates the gene transcription. In contrast, a low level of
tryptophan results in detachment of the repressor from the operator
region and allows gene expression.

Structure of Tryptophan Operon

The trp operon consists of:

 Promoter (P) region

 Operator (O) region
 Regulatory region
 Attenuator (A) region
 Structural genes (Trp A-E)
Promoter Gene

It refers to the region on a bacterial chromosome that comprises a

specific nucleotide sequence, where an RNA polymerase can
specifically bind to initiate transcription. The binding of a repressor
protein with the operator inhibits the binding of RNA polymerase with
the promoter sequence, which in turn terminates the transcription.
Operator Gene

It is the specific nucleotide sequence on chromosomal DNA of E.coli,

where a repressor protein can bind by the association of an effector
molecule or tryptophan. Here, the tryptophan molecule works as a
corepressor that aids activation of aporepressor protein.
Regulatory Gene

Tryptophan operon is a repressor system, in which a regulatory gene

of chromosome encodes trp repressor protein that recognizes the
operator sequence. The repressor protein switches on the operon
system at a low trp level in the surrounding while switches off the
system at a high trp concentration in the environment.
Therefore, a repressor protein is associated with the synthesis of five
gene products, which depends on the level of tryptophan in the
surrounding. A repressor becomes active or inactive in the presence
or absence of a corepressor or effector molecule (tryptophan).
Attenuator Region

It is found in the middle of the operator region and structural genes.

The attenuator region comprises leader sequences (160 bp in size)
that regulate the transcription via attenuation.
Its mechanism is to attenuate transcription efficiency at sufficient
tryptophan inside the bacterial cell by forming dimers. Oppositely, the
RNAp can traverse through the attenuator region and transcribe
genes necessary to build up trp at a low tryptophan level.

Structural Genes

Trp A, B, C, D and E are structural genes of the trp operon. The

structural genes encoding for the enzymes and their subunits are
necessary for tryptophan biosynthesis from chorismic acid.

 trpE encodes the enzyme Anthranilate synthase I.

 trpD encodes the enzyme Anthranilate synthase II.
 trpC encodes the enzyme N-5’-Phosphoribosyl anthranilate
isomerase and Indole-3-glycerolphosphate synthase.
 trpB encodes the enzyme tryptophan synthase-B subunit.
 trpA encodes the enzyme tryptophan synthase-A subunit.
Regulation of Tryptophan Operon
Two mechanisms regulate the trp operon.

1. Repressor or derepression mechanism

2. Attenuation mechanism
Repression of Tryptophan Operon

It occurs when the trp level is high in the surrounding medium. In this
case, the TrpR gene of the tryptophan operon releases apo-
repressor (inactive) protein that alone cannot attach to
the operator region. In the presence of a corepressor or tryptophan,
the apo-repressor protein activates and blocks the RNA polymerase.
Thus, RNAP can not initiate structural genes transcription or inhibits
enzymes necessary for the trp construction. Therefore, the respective
RNA polymerase can neither bind with the operator gene nor
transcribe structural genes at a high tryptophan concentration.
Expression of trp operon during availability of tryptophan indicates
that the operon system will switch off to terminate the transcription.

Hence, the repression of trp operon is mediated via complex formed

bythe association of an allosteric repressor and an effector
molecule. Tryptophan functions as a corepressor or an effector
molecule that transforms the inactive apo-repressor to an active
repressor, which ultimately adheres to the operator sequence to block
gene expression.

Derepression of Tryptophan Operon

It occurs in the case of low tryptophan levels in the environment.

Due to the lack of sufficient effector molecules, the active repressor
protein attached to the operator region will detach. After its
dissociation, the repressor remains inactive and functionless. As a
result, RNA polymerase becomes free to transcribe structural genes
further to produce tryptophan.

The expression of trp operon during unavailability of tryptophan

means that the operon system will switch on to conduct transcription
of structural genes by the RNA polymerase. Hence,
the derepression is achieved by the dissociation of repressor protein
due to lack of trp or effector molecules, which together can form an
active complex.

Attenuation

It is the second regulatory region of the trp operon controlled by

the trpL gene or attenuator. A leader sequence controls the gene
expression via an attenuation mechanism. It comprises a polypeptide
sequence plus an attenuator (contains palindromic sequences).

Once the bacterial DNA is transcribed into mRNA, the attenuator

sequence can form dimers due to the pairing of palindromic
sequences. There are four domains in the leader sequence, in which
domain-3 can pair with either domain-2 or domain-4, and domain-1
can pair with domain-2. Besides, it comprises two trp residues.
The pairing of domain-2 and 3 results in antitermination. Conversely,
the pairing of domain-3 and 4 causes a termination of trp
biosynthesis. The presence of domain-4 (also called attenuator) is
important to terminate the transcription because it only can
facilitate stem-loop formation. The attenuation mechanism depends
upon the pairing of the ribosome and the level of tryptophan inside a
bacterial cell.
At low tryptophan level

The ribosome sits at domain-1 of the mRNA transcript. Then, it

translates the mRNA very slowly due to the low tryptophan level. As a
result, domain-3 interacts with domain-2 due to the halt of the
ribosome at domain-1. In such a case, the stem and loop structure will
not form. As a result, the transcription may continue to synthesize
enzymes necessary for trp production.

At high tryptophan level

The ribosome rapidly translates the domain-1 and sits at the domain-2
when the concentration of tryptophan is high inside the cell. As a
result, domain-3 associates with domain-4 and aids in forming a hair-
loop structure.

The dimerization of domain-3 and 4 cause the RNAp to fall off and
prevent mRNA from transcribing genes encoding enzymes for the trp
biosynthesis. Therefore, an attenuator functions as a barrier at high
trp concentration due to the pairing of self-complementary sequences.
Conclusion

Therefore, we can conclude that the tryptophan repressor and

attenuation system decides when to switch on or switch off the
expression of genes synthesizing trp, according to the availability of
tryptophan.

Regulation of Gene Expression in Eukaryotes

Controlling gene expression in eukaryotes is more complicated and occurs at
multiple levels. Because eukaryotic genes do not have operons, each gene must be
controlled separately. Furthermore, eukaryotic cells have a much larger number of
genes than prokaryotic cells. Gene expression can be controlled at any time after
DNA is transcribed into mRNA and mRNA is translated into protein. Regulation
is broken down into five categories for ease of use: epigenetic, transcriptional,
post-transcriptional, translational, and post-translational.

Fig: Regulation of gene expression in eukaryotes can occur at five different levels.