Prokaryotic Gene Regulation

Discuss different components of prokaryotic gene regulation

The DNA of prokaryotes is organized into a circular chromosome supercoiled in the

nucleoid region of the cell cytoplasm. Proteins that are needed for a specific function
are encoded together in blocks called operons. For example, all of the genes needed to
use lactose as an energy source are coded next to each other in the lactose (or lac)
operon.

In prokaryotic cells, there are three types of regulatory molecules that can affect the
expression of operons: repressors, activators, and inducers. Repressors are proteins
that suppress transcription of a gene in response to an external stimulus,
whereas activators are proteins that increase the transcription of a gene in response to
an external stimulus. Finally, inducers are small molecules that either activate or
repress transcription depending on the needs of the cell and the availability of substrate.

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.
French scientists François Jacob (1920–2013) and Jacques Monod at the Pasteur
Institute were the first to show the organization of bacterial genes into operons, through
their studies on the lac operon of E. coli. They found that in E. coli, all of the structural
genes that encode enzymes needed to use lactose as an energy source lie next to each
other in the lactose (or lac) operon under the control of a single promoter,
the lac promoter. For this work, they won the Nobel Prize in Physiology or Medicine in
1965.

Although eukaryotic genes are not organized into operons, prokaryotic operons are
excellent models for learning about gene regulation generally. There are some gene
clusters in eukaryotes that function similar to operons. Many of the principles can be
applied to eukaryotic systems and contribute to our understanding of changes in gene
expression in eukaryotes that can result pathological changes such as cancer.

Each operon includes DNA sequences that influence its own transcription; these are
located in a region called the regulatory region. The regulatory region includes the
promoter and the region surrounding the promoter, to which transcription factors,
proteins encoded by regulatory genes, can bind. Transcription factors influence the
binding of RNA polymerase to the promoter and allow its progression to transcribe
structural genes. A repressor is a transcription factor that suppresses transcription of a
gene in response to an external stimulus by binding to a DNA sequence within the
regulatory region called the operator, which is located between the RNA polymerase
binding site of the promoter and the transcriptional start site of the first structural gene.
Repressor binding physically blocks RNA polymerase from transcribing structural
genes. Conversely, an activator is a transcription factor that increases the transcription
of a gene in response to an external stimulus by facilitating RNA polymerase binding to
the promoter. An inducer, a third type of regulatory molecule, is a small molecule that
either activates or represses transcription by interacting with a repressor or an activator.
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.
The trp Operon: A Repressor Operon
Bacteria such as E. coli need amino acids to survive. Tryptophan is one such amino
acid that E. coli can ingest from the environment. E. coli can also synthesize tryptophan
using enzymes that are encoded by five genes. These five genes are next to each other
in what is called the tryptophan (trp) operon (Figure 1). If tryptophan is present in the
environment, then E. coli does not need to synthesize it and the switch controlling the
activation of the genes in the trp operon is switched off. However, when tryptophan
availability is low, the switch controlling the operon is turned on, transcription is initiated,
the genes are expressed, and tryptophan is synthesized.
A DNA sequence that codes for proteins is referred to as the coding region. The five
coding regions for the tryptophan biosynthesis enzymes are arranged sequentially on
the chromosome in the operon. Just before the coding region is the transcriptional
start site. This is the region of DNA to which RNA polymerase binds to initiate
transcription. The promoter sequence is upstream of the transcriptional start site; each
operon has a sequence within or near the promoter to which proteins (activators or
repressors) can bind and regulate transcription.
A DNA sequence called the operator sequence is encoded between the promoter
region and the first trp coding gene. This operator contains the DNA code to which the
repressor protein can bind. When tryptophan is present in the cell, two tryptophan
molecules bind to the trp repressor, which changes shape to bind to the trp operator.
Binding of the tryptophan–repressor complex at the operator physically prevents the
RNA polymerase from binding, and transcribing the downstream genes.
When tryptophan is not present in the cell, the repressor by itself does not bind to the
operator; therefore, the operon is active and tryptophan is synthesized. Because the
repressor protein actively binds to the operator to keep the genes turned off,
the trp operon is negatively regulated and the proteins that bind to the operator to
silence trp expression are negative regulators.
Catabolite Activator Protein (CAP): An Activator Regulator
Just as the trp operon is negatively regulated by tryptophan molecules, there are
proteins that bind to the operator sequences that act as a positive regulator to turn
genes on and activate them. For example, when glucose is scarce, E. coli bacteria can
turn to other sugar sources for fuel. To do this, new genes to process these alternate
genes must be transcribed. When glucose levels drop, cyclic AMP (cAMP) begins to
accumulate in the cell. The cAMP molecule is a signaling molecule that is involved in
glucose and energy metabolism in E. coli. When glucose levels decline in the cell,
accumulating cAMP binds to the positive regulator catabolite activator protein (CAP),
a protein that binds to the promoters of operons that control the processing of
alternative sugars. When cAMP binds to CAP, the complex binds to the promoter region
of the genes that are needed to use the alternate sugar sources (Figure 1). In these
operons, a CAP binding site is located upstream of the RNA polymerase binding site in
the promoter. This increases the binding ability of RNA polymerase to the promoter
region and the transcription of the genes.
The lac Operon: An Inducer Operon
The third type of gene regulation in prokaryotic cells occurs through inducible operons,
which have proteins that bind to activate or repress transcription depending on the local
environment and the needs of the cell. The lac operon is a typical inducible operon. As
mentioned previously, E. coli is able to use other sugars as energy sources when
glucose concentrations are low. To do so, the cAMP–CAP protein complex serves as a
positive regulator to induce transcription. One such sugar source is lactose.
The lac operon encodes the genes necessary to acquire and process the lactose from
the local environment. CAP binds to the operator sequence upstream of the promoter
that initiates transcription of the lac operon. However, for the lac operon to be activated,
two conditions must be met. First, the level of glucose must be very low or non-existent.
Second, lactose must be present. Only when glucose is absent and lactose is present
will the lac operon be transcribed. This makes sense for the cell, because it would be
energetically wasteful to create the proteins to process lactose if glucose was plentiful
or lactose was not available.

Prokaryotic Gene Regulation at Work

As we’ve just learned, there are three types of regulatory molecules that can affect the
expression of operons: repressors, activators, and inducers.

 Repressors are proteins that suppress transcription of a gene in response to an

external stimulus. In other words, a repressor keeps a gene “off.”
 Activators are proteins that increase the transcription of a gene in response to an
external stimulus. In other words, an activator turns a gene “on.”
 Inducers are small molecules that either activate or repress transcription
depending on the needs of the cell and the availability of substrate. Inducers
basically help speed up or slow down “on” or “off” by binding to a repressor or
activator. In other words: they don’t work alone.