Gene Regulation and Operon

Assignment # 2

Name: Yeshua Sagar Shahzad

Roll No.: 11
Registration No.: BBT193003
Date: 27-03-20
Subject: Molecular Genetics
Submitted to: Sir Shoukat Iqbal
 “Introduction”

Gene regulation
Gene regulation is the process of controlling which genes in a cell's DNA are
expressed (used to make a functional product such as a protein). Different cells in a multicellular
organism may express very different sets of genes, even though they contain the same DNA.
Gene regulation is essential for viruses, prokaryotes and eukaryotes as it increases the versatility
and adaptability of an organism by allowing the cell to express protein when needed. Although as
early as 1951, Barbara McClintock showed interaction between two genetic loci, Activator (Ac)
and Dissociator (Ds), in the color formation of maize seeds, the first discovery of a gene regulation
system is widely considered to be the identification in 1961 of the lac operon, discovered by
François Jacob and Jacques Monod, in which some enzymes involved in lactose metabolism are
expressed by E. coli only in the presence of lactose and absence of glucose.
Cells express (transcribe and translate) only a subset of their genes. Cells respond and adapt to
environmental signals by turning on or off expression of appropriate genes. In multicellular
organisms, cells in different tissues and organs differentiate, or become specialized by making
different sets of proteins, even though all cells in the body (with a couple of exceptions) have the
same genome. Such changes in gene expression, or differential gene expression among cells, are
most often regulated at the level of transcription.
There are three broad levels of regulating gene expression:
1. transcriptional control (whether and how much a gene is transcribed into mRNA)
2. translational control (whether and how much an mRNA is translated into protein)
3. post-translational control (whether the protein is in an active or inactive form, and whether
the protein is stable or degraded)

Gene regulation in prokaryotes

In bacteria and archaea, structural proteins with related functions—such as the genes that encode
the enzymes that catalyze the many steps in a single biochemical pathway—are usually encoded
together within the genome in a block called an operon and are transcribed together under the
control of a single promoter. This forms a polycistronic transcript (Figure 1). The promoter then
has simultaneous control over the regulation of the transcription of these structural genes because
they will either all be needed at the same time, or none will be needed.
In prokaryotes, there are examples of operons whose gene products are required rather consistently
and whose expression, therefore, is unregulated. Such operons are constitutively expressed,
meaning they are transcribed and translated continuously to provide the cell with constant
intermediate levels of the protein products. Such genes encode enzymes involved in housekeeping
functions required for cellular maintenance, including DNA replication, repair, and expression, as
well as enzymes involved in core metabolism. In contrast, there are other prokaryotic operons that
are expressed only when needed and are regulated by repressors, activators, and inducers.

Gene regulation in eukaryotes

Eukaryotic genes also have promoters to which RNA polymerase binds. The
fundamental mechanism underlying binding of RNA polymerase to the promoter is similar to that
in prokaryotes, but it is considerably more complicated. Eukaryotes have many proteins called
general transcription factors, including those that recognize specific sequences such as TATA,
and binding of these factors promotes binding of RNA polymerase. In general, the specific DNA
sequences involved in transcriptional regulation, including promoters, are called “cis elements,”
and the proteins that bind to these cis elements to regulate their expression are called “trans
factors.”
In addition to this fundamental system, transcriptional regulatory regions called enhancers and
silencers change expression of various genes according to various changes in intra- and
extracellular conditions. These regions are cis elements with specific sequences, and some proteins
(trans factors) recognized bind to them. When an enhancer-binding protein binds to the enhancer,
binding of RNA polymerase to the promoter increases and a significant increase in gene expression
is observed. Conversely, silencers inhibit gene expression.
Differences in the Regulation of Gene Expression of Prokaryotic and
Eukaryotic Organisms
Prokaryotic organisms Eukaryotic organisms
Lack nucleus Contain nucleus
DNA is found in the cytoplasm DNA is confined to the nuclear compartment
RNA transcription and protein formation occur RNA transcription occurs prior to protein
almost simultaneously formation, and it takes place in the nucleus.
Translation of RNA to protein occurs in the
cytoplasm.
Gene expression is regulated primarily at the Gene expression is regulated at many levels
transcriptional level (epigenetic, transcriptional, nuclear shuttling,
post-transcriptional, translational, and post-
translational)

Gene Regulation mechanism

Mechanisms of gene regulation include:
• Regulating the rate of transcription. This is the most economical method of regulation.
• Regulating the processing of RNA molecules, including alternative splicing to produce
more than one protein product from a single gene.
• Regulating the stability of mRNA molecules.
• Regulating the rate of translation.
Gene regulation makes cells different
Gene regulation is how a cell controls which genes, out of the many genes in its genome, are
“turned on” (expressed). Thanks to gene regulation, each cell type in your body has a different set
of active genes—despite the fact that almost all the cells of your body contain the exact same
DNA. These different patterns of gene expression cause your various cell types to have different
sets of proteins, making each cell type uniquely specialized to do its job.
For example, one of the jobs of the liver is to remove toxic substances like alcohol from the
bloodstream. To do this, liver cells express genes encoding subunits (pieces) of an enzyme called
alcohol dehydrogenase. This enzyme breaks alcohol down into a non-toxic molecule. The neurons
in a person’s brain don’t remove toxins from the body, so they keep these genes unexpressed, or
“turned off.” Similarly, the cells of the liver don’t send signals using neurotransmitters, so they
keep neurotransmitter genes turned off (Figure 1).

EVOLUTION OF GENE REGULATION

Prokaryotic cells can only regulate gene expression by controlling the amount of transcription. As
eukaryotic cells evolved, the complexity of the control of gene expression increased. For example,
with the evolution of eukaryotic cells came compartmentalization of important cellular
components and cellular processes. A nuclear region that contains the DNA was formed.
Transcription and translation were physically separated into two different cellular compartments.
It therefore became possible to control gene expression by regulating transcription in the nucleus,
and also by controlling the RNA levels and protein translation present outside the nucleus.
Some cellular processes arose from the need of the organism to defend itself. Cellular processes
such as gene silencing developed to protect the cell from viral or parasitic infections. If the cell
could quickly shut off gene expression for a short period of time, it would be able to survive an
infection when other organisms could not. Therefore, the organism evolved a new process that
helped it survive, and it was able to pass this new development to offspring.
Gene regulation and differences between species

Differences in gene regulation makes the different cell types in a multicellular organism (such as
yourself) unique in structure and function. If we zoom out a step, gene regulation can also help us
explain some of the differences in form and function between different species with relatively
similar gene sequences.
For instance, humans and chimpanzees have genomes that are about 98.8\%98.8%98, point, 8,
percent identical at the DNA level. The protein-coding sequences of some genes are different
between humans and chimpanzees, contributing to the differences between the species. However,
researchers also think that changes in gene regulation play a major role in making humans and
chimps different from one another. For instance, some DNA regions that are present in the
chimpanzee genome but missing in the human genome contain known gene-regulatory sequences
that control when, where, or how strongly a gene is expressed

Operon
Operon, genetic regulatory system found in bacteria and their viruses in which genes
coding for functionally related proteins are clustered along the DNA. This feature allows protein
synthesis to be controlled coordinately in response to the needs of the cell. By providing the means
to produce proteins only when and where they are required, the operon allows the cell to conserve
energy (which is an important part of an organism’s life strategy).
A typical operon consists of a group of structural genes that code for enzymes involved in a
metabolic pathway, such as the biosynthesis of an amino acid. These genes are located
contiguously on a stretch of DNA and are under the control of one promoter (a short segment of
DNA to which the RNA polymerase binds to initiate transcription). A single unit of messenger
RNA (mRNA) is transcribed from the operon and is subsequently translated into separate proteins.
The promoter is controlled by various regulatory elements that respond to environmental cues.
One common method of regulation is carried out by a regulator protein that binds to the operator
region, which is another short segment of DNA found between the promoter and the structural
genes. The regulator protein can either block transcription, in which case it is referred to as a
repressor protein; or as an activator protein it can stimulate transcription. Further regulation occurs
in some operons: a molecule called an inducer can bind to the repressor, inactivating it; or a
repressor may not be able to bind to the operator unless it is bound to another molecule, the
corepressor. Some operons are under attenuator control, in which transcription is initiated but is
halted before the mRNA is transcribed. This introductory region of the mRNA is called the leader
sequence; it includes the attenuator region, which can fold back on itself, forming a stem-and-loop
structure that blocks the RNA polymerase from advancing along the DNA.

The operon theory was first proposed by the French microbiologists François Jacob and Jacques
Monod in the early 1960s. In their classic paper they described the regulatory mechanism of the
lac operon of Escherichia coli, a system that allows the bacterium to repress the production of
enzymes involved in lactose metabolism when lactose is not available.

General structure of operon

1: RNA Polymerase, 2: Repressor, 3: Promoter, 4: Operator, 5: Lactose, 6: lacZ, 7: lacY, 8: lacA. Top: The gene is essentially
turned off. There is no lactose to inhibit the repressor, so the repressor binds to the operator, which obstructs the RNA polymerase
from binding to the promoter and making lactase. Bottom: The gene is turned on. Lactose is inhibiting the repressor, allowing the
RNA polymerase to bind with the promoter, and express the genes, which synthesize lactase. Eventually, the lactase will digest all
of the lactose, until there is none to bind to the repressor. The repressor will then bind to the operator, stopping the manufacture of
lactase.

An operon is made up of 3 basic DNA components:

 • Promoter – a nucleotide sequence that enables a gene to be transcribed. The promoter is
recognized by RNA polymerase, which then initiates transcription. In RNA synthesis,
promoters indicate which genes should be used for messenger RNA creation – and, by
extension, control which proteins the cell produces.
• Operator – a segment of DNA to which a repressor binds. It is classically defined in the lac
operon as a segment between the promoter and the genes of the operon.[14] The main operator (O1)
in the
lac operon is located slightly downstream of the promoter; two additional operators,
O1 and O3 are located at -82 and +412, respectively. In the case of a repressor, the repressor
protein physically obstructs the RNA polymerase from transcribing the genes.
• Structural genes – the genes that are co-regulated by the operon.

The lac operon

The lac operon of the model bacterium Escherichia coli was the first operon to be discovered and
provides a typical example of operon function. It consists of three adjacent structural genes, a
promoter, a terminator, and an operator. The lac operon is regulated by several factors including
the availability of glucose and lactose. It can be activated by allolactose. Lactose binds to the
repressor protein and prevents it from repressing gene transcription. This is an example of the
derepressible (from above: negative inducible) model.So it is a negative inducible operon induced
by presence of lactose or allolactose.
The trp operon
Discovered in 1953 by Jacques Monod and colleagues, the trp operon in E. coli was the first
repressible operon to be discovered. While the lac operon can be activated by a chemical
(allolactose), the tryptophan (Trp) operon is inhibited by a chemical (tryptophan). This operon
contains five structural genes: trp E, trp D, trp C, trp B, and trp A, which encodes tryptophan
synthetase. It also contains a promoter which binds to RNA polymerase and an operator which
blocks transcription when bound to the protein synthesized by the repressor gene (trp R) that binds
to the operator. In the lac operon, lactose binds to the repressor protein and prevents it from
repressing gene transcription, while in the trp operon, tryptophan binds to the repressor protein
and enables it to repress gene transcription. Also unlike the lac operon, the trp operon contains a
leader peptide and an attenuator sequence which allows for graded regulation.[16] This is an example of the
corepressible model.
Predicting the number and organization of operons
The number and organization of operons has been studied most critically in E. coli. As a result,
predictions can be made based on an organism's genomic sequence.
One prediction method uses the intergenic distance between reading frames as a primary predictor
of the number of operons in the genome. The separation merely changes the frame and guarantees
that the read through is efficient. Longer stretches exist where operons start and stop, often up to
40–50 bases.
An alternative method to predict operons is based on finding gene clusters where gene order and
orientation is conserved in two or more genomes.
Operon prediction is even more accurate if the functional class of the molecules is considered.
Bacteria have clustered their reading frames into units, sequestered by co-involvement in protein
complexes, common pathways, or shared substrates and transporters. Thus, accurate prediction
would involve all of these data, a difficult task indeed.

Operon concept in gene regulation

A typical operon consists of a group of structural genes that code for enzymes involved in a
metabolic pathway, such as the biosynthesis of an amino acid. These genes are located
contiguously on a stretch of DNA and are under the control of one promoter (a short segment of
DNA to which the RNA polymerase binds to initiate transcription). A single unit of messenger
RNA (mRNA) is transcribed from the operon and is subsequently translated into separate proteins.
The promoter is controlled by various regulatory elements that respond to environmental cues.
One common method of regulation is carried out by a regulator protein that binds to the operator
region, which is another short segment of DNA found between the promoter and the structural
genes. The regulator protein can either block transcription, in which case it is referred to as a
repressor protein; or as an activator protein it can stimulate transcription. Further regulation occurs
in some operons: a molecule called an inducer can bind to the repressor, inactivating it; or a
repressor may not be able to bind to the operator unless it is bound to another molecule, the
corepressor. Some operons are under attenuator control, in which transcription is initiated but is
halted before the mRNA is transcribed. This introductory region of the mRNA is called the leader
sequence; it includes the attenuator region, which can fold back on itself, forming a stem-and-loop
structure that blocks the RNA polymerase from advancing along the DNA.
Conclusion
Genes are turned off and on to respond changing enviromental conditions. There are many points
of control such as modifying the DNA or how long the mRNA will last. The comomn example is
operon (lac operon ). Current genomic revolution has unlocked the potential to understand the gene
regulation at molecular, cellular and physiological levels. The first step in this process is to identify
the genes present in a genome and study the expression patterns of the gene influenced by
regulatory signals. Several programs are available in the public domain that can identify genes
from the DNA sequence using ‘signals’ and ‘contents’ of the DNA sequence. Gene prediction
programs using ‘contents’ information are limited from identifying only protein coding genes in
the genome.

References:
• www.britannica.com
• www.ncbi.nlm.nih.gov
• www.healio.com
• www.nature.com
• https://en.wikipedia.org/
• https://www.khanacademy.org