Control of Gene Expression in Prokaryotes

Gene regulation, an inherent property of all organisms, is responsible for an organism's ability to
respond to changes in the environment. Transcriptional gene regulations allow bacteria to express genes
only when they are needed. In bacterial cells, the most common arrangement of genes has a powerful
and appealing logic: genes devoted to a single metabolic goal, say the synthesis of the amino acid
tryptophan are found in a continuous linear array in the bacterial DNA. This gene order makes it
possible to produce a continuous strand RNA that carries the message for a related series of enzymes
devoted to making tryptophan. Each section of the mRNA represents the unit (or gene) that instructs
the protein-synthesizing apparatus to make a particular protein. Such an arrangement of genes in a
functional group is called an operon because it can be operated as a unit by one decision to make mRNA
from the entire operon i.e. an operon is a co-transcribed and co-regulated contiguous set of genes. It is
a cluster of genes under the control of a single regulatory signal or promoter. The operon system in
bacteria is well defined and has been widely investigated. The gene order, gene content and regulatory
mechanisms of operons can be very different, even in closely related species.
A typical bacterial cell contains several thousand genes. Some genes perform general functions and
remain active all the time. Thus, their expressions occur constitutively, meaning that they are expressed
at a reasonably constant rate and not subject to regulation. These genes are referred to as housekeeping
genes. Genes coding for rRNAs and synthesis of proteins involved in translation—are examples of
housekeeping genes. Most genes are often expressed only when their products are required. Constitutive
expression of such genes would be wasteful because that energy could otherwise be utilized for useful
work. Expression of such genes is regulated in such a manner that these genes give products only when
and where they are needed. According to the cell’s requirement, the expression of such genes for their
product varies. There are various stages at which the expression of a gene can be regulated. In a
prokaryote, the most common step at which the regulation of a gene expression occurs is the
transcription initiation. It is energetically the most efficient step to regulate gene expression.
Transcriptional regulation also occurs at steps after initiation, specifically during elongation and
termination. Prokaryotic transcriptional regulation is accomplished by gene regulatory proteins which
bind with regulatory sequences located near the transcription start site of a transcription unit. Gene
regulatory proteins, the products of regulatory genes, are of two types – activator and repressor. The
binding of an activator to its target regulatory sequence (located near the promoter) increases the rate
of transcription. Such regulations are referred to as positive regulation because it is required to increase
the rate of transcription. The binding of the repressor to its target regulatory sequence (called the
operator, located near the transcription start site) prevents a gene from being expressed. Because
binding of a repressor prevents the gene expression, it is referred to as negative regulation.
Inducible and repressible system
Not all of the proteins a bacterial cell can produce are needed at all times and also in the same quantities.
For example, enzymes for breakdown of sugars such as lactose may not be required if lactose is not

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present in the cell’s environment. If a given metabolite is not present, enzymes for its breakdown are
not required, and synthesizing these enzymes is wasteful. If the cell produces enzymes for the
degradation of a particular compound only when this compound is present in the environment, the
system is known as an inducible system. The best-studied inducible system is the catabolic degradation
of the disaccharide lactose in E. coli.
On the other hand, in the anabolic process such as tryptophan synthesis enzymes are required for
synthesis. But if tryptophan is already present in adequate quantity in the cell’s environment, then
enzymes for tryptophan synthesis are not required. If the cell produces enzymes for the synthesis of a
particular compound only when this compound is not present in the environment, the system is known
as a repressible system. The best-studied repressible system is the synthesis of amino acid tryptophan
in E. coli.
Genes that encode enzymes involved in catabolic pathways often are expressed only in the presence of
the substrates of the enzymes; their expression is inducible. Genes that encode enzymes involved in
anabolic pathways usually are turned off in the presence of the end product of the pathway; their
expression is repressible.
lac operon in E. coli
Lactose (milk sugar) is a β-galactoside that E. coli can use for energy and as a carbon source after it is
broken down into glucose and galactose. It is metabolized by the products of lactose (lac) operon, which
consists of an operator, a promoter and three structural genes.

Figure: The lac operon includes a promoter (P), an operator (O) and three structural genes– the lacZ,
lacY and lacA. It is transcribed as a multigenic (polycistronic) mRNA. The mRNA transcript is then
translated as individual proteins. Both the operon and the regulator gene have their own promoters.

The lac operator is a short region of DNA that interacts with a regulatory protein Lac repressor, which
negatively controls the transcription of the operon. lacZ codes for the enzyme β-galactosidase that
cleaves the lactose molecule to yield glucose and galactose. This enzyme also converts lactose to
allolactose. There are very few molecules of β-galactosidase in a wild-type E. coli cell grown in the
absence of lactose. After adding lactose to the medium, however, this enzyme increases in concentration
within the bacterial cell.

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lacY codes for the β-galactoside permease, which transports lactose into the cell. lacA codes for β-
galactoside acetyltransferase (or β-galactoside transacetylase). This enzyme is not essential for lactose
metabolism but appears to play a role in the detoxification of compounds by transferring an acetyl group
from acetyl-CoA to β-galactoside.
All three structural genes of the lac operon are transcribed into a single, multigenic (polycistronic)
mRNA molecule. Regulation of the transcription of this mRNA controls the synthesis of all three
enzymes. This operon is controlled by both positive and negative regulation.
Negative regulation of lac operon
In the absence of lactose (inducer), the Lac repressor (product of lacI gene) binds to the lac operator
and prevents transcription initiation of the lac operon. Because binding of an active repressor prevents
the transcription, it is termed negative regulation. The Lac repressor molecule is a negative regulator.
The effect of Lac repressor’s binding to the operator is to block the transcription. Consequently, all of
the structural genes of the lac operon (the lacZ, lacY and lacA genes) are repressed, and there is very
less amount of β-galactosidase, β-galactoside permease or transacetylase in the cell.
But how does the presence of the inducer trigger the expression of lac operon? When an inducer is
present, it binds to the allosteric site of the Lac repressor, thereby inactivating its operator binding site.
However, lactose does not have this effect; rather, allolactose does. Allolactose is thus referred to as the
actual inducer of the lac operon. Formation of allolactose is also catalyzed by the β-galactosidase.
Inactivation (mutation) of Lac repressor permits the induction (i.e. constitutive expression of structural
genes even in the absence of lactose) of transcription of the structural genes of the lac operon and,
through the translation of the polycistronic mRNA, the enzymes β-galactosidase, β-galactoside
permease and transacetylase appear in the cell in a coordinated fashion.

Figure: Galactosidase catalyzes the hydrolysis of lactose into glucose and galactose and also its
isomerization to Allolactose

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Isopropylthiogalactoside (IPTG), a synthetic non-metabolizable analogue of the lactose, also acts as an
inducer. It is an example of a gratuitous inducer, an inducer that is capable of inducing the lac operon
while not itself serving as a substrate for β-galactosidase.

Figure: Induction of lac operon. In the absence of lactose, the lac repressor binds operator and represses
transcription from the lac operon. In the presence of lactose, few molecules of the enzyme β-
galactosidase present in the cell convert lactose into allolactose. Allolactose binds to the lac repressor,
leading to the inactivation of operator binding site and to the production of lac mRNA

Positive regulation and catabolite repression

Bacteria have distinct preferences among potential carbon sources when they are offered a choice. When
glucose is available as an energy source, it is used in preference to other sugars. So, when E. coli finds
(for example) both glucose and lactose in the medium, it metabolizes the glucose and represses the use
of lactose. In the presence of both lactose and glucose, the synthesis of β-galactosidase is not induced
until all the glucose has been used up. The ability of glucose to inhibit the synthesis of certain enzymes,
referred to as the glucose effect, was recognized in bacteria by Monod. He observed that when E. coli
encounters both glucose and lactose, it metabolizes the glucose first and represses the use of lactose.
This phenomenon is due to the repressive effect of glucose on the synthesis of enzymes required for the
metabolism of other sugars. Later, the term catabolite repression was introduced as a general name for
the glucose effect. When E. coli is starved of glucose, it produces an unusual molecule, cyclic
adenosine-31,51-monophosphate (cAMP).
Catabolite repression works through an activator protein which binds to cAMP. Studies on catabolite
repression brought about the discovery of a positive regulation of transcription by the cAMP receptor
protein, CRP (also called the catabolite gene activator protein, CAP). CRP is a homodimer and acts as

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an activator. It is activated by binding of a single molecule of cAMP. It is needed for RNA polymerase
to initiate transcription of many operons of E. coli. cAMP is synthesized by the enzyme adenylate
cyclase, and its concentration is related to glucose concentration. So, when the glucose level in the cell
is high, the cAMP concentration is low. Conversely, when the glucose level is low, the cAMP
concentration is high. By itself, CAP cannot bind to the CAP binding site of the lac operon. However,
by binding to its allosteric effector, cAMP, CAP is able to bind to the CAP binding site and activate
transcription. Thus, maximum transcription from the lac operon requires the presence of the cAMP-
CAP complex

Figure: Catabolite repression of the lac operon. Only under conditions of low glucose concentration,
cAMP synthesis occurs. When cAMP is present, it forms a complex with CAP that activates
transcription by binding to a region adjacent to the lac promoter. CAP recruit’s polymerase to the lac
promoter.

Figure: Expression of the lac operon. The presence or absence of the sugars lactose and glucose control
the level of expression of the lac operon. Above basal levels of expression require the presence of
lactose (and hence, the absence of the functional Lac repressor) and absence of the preferred energy
source, glucose (and hence, the presence of the activator CAP).

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Arabinose Operon
This operon is responsible for the breakdown of arabinose molecules in the cell. Arabinose is first
converted to ribulose by arabinose isomerase, the product of araA gene, it is then phosphorylated by
ribulokinase, the product of araB gene and finally converted to xylulose-5-phosphate via ribulose-5-
phosphate epimerase, the product of araD gene. The last product enters the pentose phosphate pathway
and yields reducing power or provides precursor metabolites for glycolysis. These 3 structural genes
have a single promoter, named PBAD and are regulated by the product of araC gene, designated as
AraC. At first glance, this operon seems to be similar to the lac operon. When arabinose is absent, AraC
is produced and gets attached to the operator. In the absence of arabinose, binding of AraC to the
operator prevents the attachment of RNA polymerase to PBAD and thus none of the genes can be
transcribed. However, when arabinose becomes available, it binds to AraC and causes a structural
change in its shape, making PBAD receptive to RNA polymerase’s attachment.

However, it was found that ara operon is actually quite different in action from that of the lac operon
based on three main facts:
i. While lac operon is usually negatively regulated by the lacI gene, ara operon is both
positively and negatively regulated by araC, depending on circumstances.
ii. Although lacI mutants cause the lac operon to be expressed constitutively, araC mutants
do not. In fact, mutations in araC lead to a “super-repressed” condition where araA, B and
D are shut down even when arabinose is abundant.
iii. Whereas constitutive mutants are frequent in a negatively regulated operon such as the lac
operon, such mutants are extremely rare in the ara operon. This showed that maybe the
constitutive phenotype in the ara operon does not have a connection to inactivation of the
araC. So, another model was hypothesized as follows:

The regulatory region of the araBAD operon can be turned on or off by the araC protein encoded by the
araC gene. This can be explained given that araC usually acts in its dimeric form and the operon has
four regulatory regions; operator region (O1 and O2) and initiator region (I1 and I2). In the absence of

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arabinose, the araC protein acts as a repressor of the operon by binding to non-adjacent sites in the
regulatory region of the operon (O & I ). This binding causes the DNA to loop and prevents RNA
2 1

polymerase from being able to access the promoter and as such, it will be unable to cause the
transcription of structural genes. When AraC binds this way, transcription of araA, B and D is repressed.

In the presence of arabinose, the araC protein undergoes a conformational change upon binding
arabinose. This causes it to act as an araBAD activator. In this scenario, araC protein after binding to
arabinose binds to adjacent half-sites I and I located between PBAD and the CAP site (see diagram).
1 2

In the absence of glucose, cAMP will bind to the CAP site upstream of the promoter. RNA polymerase
then binds to the promoter site and transcribes the structural genes. araC protein requires the presence
of both arabinose and cAMP for operon operation.

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Fig: (a) AraC protein showing its DNA binding region and arabinose binding pocket, (b) AraC in its
dimerized state bound to non-alternate regulatory regions (I1 and O2) in the absence of arabinose causing
DNA to loop in such a way that RNA polymerase cannot bind to PBAD promoter and thus preventing
the transcription of structural genes (i.e. negative regulation), (c)AraC binding to adjacent regulatory
half-site (I1 and I2) in the presence of arabinose enables RNA polymerase to position at PBAD leading
to the transcription of structural genes.

Thus, AraC is a repressor in the absence of arabinose but an activator in the presence of arabinose.
Hence, depending on the availability of arabinose, the arabinose operon can either be positively or
negatively regulated by AraC. This is unlike the lac operon which is only negatively regulated by the
lac repressor. AraC in its repressor form binds DNA with high affinity. Mutations in araC, designated
as araCC, causes decreased DNA binding affinity (recall that AraC has a DNA binding domain) making
it unable to bind the regulatory regions effectively thus resulting in a super-repressed state even when
arabinose is present.

The Trp Operon-A Repressor Operon

Bacteria such as E. coli need amino acids to survive. Tryptophan is one such amino acids 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. If

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tryptophan is present in the environment, then E. coli does not need to synthesize it; the switch
controlling the activation of the genes in the trp operon is turned 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. The tryptophan operon consists of five structural genes:
trpE, trpD, trpC, trpB and trpA that code for enzymes involved in the conversion of chorismic acid to
tryptophan (trpE and trpD code for anthranilate synthase, trpC for indoleglycerol phosphate synthase
and trpB & trpA code for tryptophan synthase). The controlling site in trp operon lies next to trpE and
consists of a promoter site (P), an overlapping operator site (O), and a leader region, trpL that codes for
a leader peptide and an RNA attenuator. The leader peptide is involved in the attenuation mechanism.

Fig: Tryptophan Operon in E. coli. Trp operon contains five structural genes: trpE, trpD, trpC, trpB and
trpA. It also contains a promoter (P) where RNA polymerase binds, an operator (O) where Trp repressor
binds and a leader region, trpL that codes for a leader peptide and an RNA attenuator

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. In this repressible operon, the product
of the trpR gene, the Trp repressor, is inactive by itself (called aporepressor); it does not recognize the
operator sequence of the trp operon. The repressor only becomes active when it combines with
tryptophan. Hence, in the absence of tryptophan, the aporepressor (inactive regulatory protein) has no
effect on the tryptophan operon. Consequently, the enzymes for synthesizing the amino acid are
produced and the cell makes tryptophan. Tryptophan is, thus, referred to as the corepressor since it acts
as an effector to convert the aporepressor into the active repressor. When tryptophan binds to the
aporepressor, it induces a conformational change that converts the regulatory protein into the active
holorepressor. The holorepressor binds to the operator and blocks the attachment of RNA polymerase
to a promoter. This shuts off the transcription of the structural genes.

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Fig: The repressor-corepressor complex binds at the operator and prevents the transcription of the trp
operon in E. coli. Without the corepressor, the repressor cannot bind, and therefore transcription is not
prevented

Transcriptional attenuation
An additional mechanism termed transcriptional attenuation also negatively regulates the expression of
many operons in bacteria by controlling the ability of RNA polymerase to continue elongation past
specific sites. Transcriptional attenuation is carried out by two different processes– Translation-
mediated and RNA-binding protein mediated.

Translation mediated transcriptional attenuation

In E. coli, translation-mediated transcriptional attenuation provides an additional level of control that
results in more stringent regulation that could be achieved by repression of transcription initiation alone.
In trp operon, the site of attenuation is located downstream of the transcription start site. If tryptophan
is abundant, most transcription terminates at this site; only when tryptophan is scarce does transcription
continue to yield functional trp mRNA. The leader sequence (162 bp) of the operon has a fourteen-
codon open reading frame that includes two codons of tryptophan. This short coding sequence codes
for a leader peptide of fourteen amino acids. The mechanism of translation-mediated attenuation
depends on the fact that translation in bacteria is coupled with transcription, so ribosomes begin
translating the 51-end of a mRNA while it is still being synthesized. Thus, the rate of translation can
affect the structure of the growing RNA chain, which in turn determines whether further transcription
can continue. Transcription termination is signalled by a stem-loop structure that forms by
complementary base pairing between two specific sequences of the growing trp mRNA chain. This

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structure forms if the translation of the growing chain is proceeding at a normal rate, as it does when
tryptophan is present in adequate supply. If tryptophan is scarce, however, protein synthesis stalls at a
critical region of the message. If this occurs, the ribosomes bound to the mRNA block formation of the
transcription-terminating stem-loop, allowing trp mRNA synthesis to continue.

Fig: Attenuation in Trp Operon

The leader sequence called trpL has four stretches of RNA (region 1, 2, 3 and 4) that can base pair with
each other in different combinations. The critical region of trp mRNA (region 1) contains two adjacent
tryptophan codons, so the rate of translation is highly dependent on tryptophan levels; this is the link
between transcriptional attenuation and the availability of tryptophan. If tryptophan levels in the cell is
high, ribosome quickly progresses pass region 1 and reaches region 2. When ribosome reaches region
2, it prevents it from base pairing with region 3. Region 3 then forms a base pair with region 4 thus
resulting in the formation of a terminator stem-loop. This causes the release of RNA polymerase from
the mRNA. The released RNA polymerase thus prevents transcription of structural genes for synthesis
of tryptophan i.e. translation continues and transcription terminates. However, if tryptophan is low,
ribosome stalls at region 1 causing region 2 to form base pair with region 3. This results in the formation
of an antiterminator stem-loop and as such, transcription of mRNA for the synthesis of tryptophan
continues.

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Fig: Mechanism of attenuation in E. coli Trp Operon. When tryptophan is plentiful, translation of the short leader
peptide encoded by trpL proceeds, the terminator loop between regions 3 and 4 forms, and transcription
terminates. When tryptophan levels are depleted, translation of the short leader peptide stalls at region 1, allowing
regions 2 and 3 to form an antiterminator loop, and RNA polymerase can transcribe the structural genes of
the trp operon.

Lambda (λ) Phage

Bacteriophage λ is a virus that preys upon E.coli. E.coli are gram -ve bacteria having an outer
membrane, a cell wall and a cytoplasmic membrane. Bacteriophage λ is an obligate parasite so in order
to reproduce, it must inject its DNA into a host cell. First, it must get its genome past out of the bacteria
membrane. It does this via the protein Maltoporin which normally recognizes maltose and enable the
viral DNA pass through both the outer membrane and through the cell wall. To get shuttled through the
cytoplasmic membrane, it uses the phosphotransferase system (PTS). Once the viral genome is inside
its new unsuspecting host, it circularizes. At this point, two possible processes can take place; the
prophage (lysogeny) pathway which allows the bacteria to live or the lytic pathway which leads to its
death.
In the prophage pathway, the viral DNA integrates into the host genome and at this point, it is termed a
latent prophage. The host unsuspecting replicates over and over taking the viral genome with it.
However in the lytic pathway, the circularized bacteriophage λ DNA gets busy using the E.coli’s
replication machinery and resources to make many copies of itself after which the host cell (E.coli)
ruptures to release new bacteriophage which infects more host cells.

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Although the bacterium in the prophage pathway doesn’t get ruptured, after so many replicative cycles,
an induction event (DNA damage caused by agents such as UV light or mitomycin C) will cause a shift
from the lysogenic pathway to the lytic pathway in one of the E.coli’s progenies. Thanks to two genes
(cro and c1), the virus can decide to stay in the lytic or lysogenic phase. When c1 is active, cro is
repressed and vice versa. When c1 produces its mRNA, it is translated into a protein that acts on the
operators to inhibit cro and activate the c1 gene. When c1 is active, most of the lambda DNA remains
untranscribed. When cro is transcribed, the translated mRNA becomes a protein that spells the E.coli’s
doom. This protein also acts on the operator to activate the cro gene causing yet more protein to be
produced and, in this state, most of the viral DNA gets transcribed. This protein also inhibits c1 gene.
As a result, the bacterium turns into a workhouse for the virus until its death at which point it spreads
the virus to another unsuspecting host.

Lambda Phage and its decision-making process; lytic and lysogenic growth
The genome of the lambda phage has two promoters that will result in the expression of proteins to put
the virus in lytic or lysogenic growth. Two promoters; PR and PL for rightward and leftward promoter
respectively are responsible for this. PR and PL are strong promoters which express cro and N
respectively while PRM is a weak promoter that expresses c1.

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PR expresses rightward and it expresses Cro while PL expresses leftward and it expresses N
(antitermination). When we have a polymerase that is transcribing, it will normally stop when it is
indicated to so i.e. it stops at the stop signal. However, when we have an antitermination, it skips the
stop signal and goes further so as to end up with a longer transcript. PRM is the promoter in the middle
of PR and PL and it expresses leftward as well where it expresses c1 also known as the lambda repressor.
When PR and PL are in operation, the virus will be in lytic growth. However, when PRM is in operation,
the virus will be in lysogenic growth. PR and PL have three operator sequences. The promoters; PR and
PRM overlap between these three operator sequences; OR3, OR2 & OR1 in the viral genome. The proteins
that signal lytic or lysogenic growth bind to these operator sequences at different affinities.
C1: OR1 > OR2 = OR3
Cro: OR3 > OR2 = OR1
These operator sequences are binding sites for the OR repressor.

As shown above, the promoters conveniently overlap with the operator sequences. PR overlaps with OR1
and PRM overlaps with OR3 i.e. if we have PR forming Cro which binds with high affinity with OR3, it is
essentially on the way of PRM i.e. it blocks PRM. RNA polymerase will thus be unable to go bind PRM
because PRM has been completely blocked by Cro. RNA polymerase can thus only bind the other
promoter PR and express rightwards making more Cro and causing the virus to remain in lytic growth.

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In the same vein, when PRM expresses C1 (lambda repressor), they activate one another with their
tetramerization region. Recall that C1 binds OR1 with highest affinity and OR2 cooperatively, it will
thus be in the way of PR thereby making RNA polymerase unable to bind PR therefore putting the virus
in lysogenic growth.

The role of c11 protein in the switch from lytic to lysogenic growth
Recall that PR and PL are strong promoters and PRM is a weak promoter. Therefore, once there is an
infection from a bacteriophage to E. coli, lytic growth is induced. N is the first gene transcribed from
PL, from which RNA polymerase transcribes in a leftward direction. The product of N, called pN or N
protein (antiterminator), prevents RNA polymerase from stopping at terminator sites from P L and PR.

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Aside from N and cro, this will cause the expression of also c111 protein on the left and c11 protein on
the right.

The c11 product is an unstable protein. A protease encoded by the hflA gene on the E. coli
chromosome will degrade the c11 protein. Mutations in hflA cause a high frequency of lysogeny
(do you see why?), hence the acronym for its name. The bacteriophage  protein encoded by
the c111 gene will interfere with degradation of the c11 protein by HflA. Hence, c111 stabilizes
c11. Mutations in hflA will cause a high frequency of lysogeny because the gene product (i.e.
protease formed from the mutant gene) is unable to degrade c11 nor c111 (What then is the role
of c11?)
c11 when expressed binds to c11 binding site which is close to PRE; another promoter which expresses
leftward. It however requires c11 to bind to the c11 binding site first because PRE is an extremely weak
promoter. Binding of c11 to c11 binding site is what helps position RNA polymerase at PRE so that it
can properly express leftwards. PRE however doesn’t make cro but rather antisense cro because it is in
the opposite direction. It also expresses pass c1 thus resulting in the expression of the lambda repressor
C1.

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If we have enough C1 being made, C1 binds to OR1 with high affinity thereby blocking PR. Because PR
is blocked, RNA polymerase positions at PRM instead making more C1 which causes the virus to switch
into lysogenic growth. The switch thus happens because of c11 essentially. Whereas C1 repressor is
required to maintain the repressed lysogenic state, the C11 and C111 proteins are only required to
initially activate C1 synthesis. Once C1 has been made, the c11 and c111 functions are no longer
required because C1 can maintain its own synthesis.
DNA damage by UV light and carcinogens (induction event) will cause the activation of DNA repair
mechanisms. It also results in the cleavage of  repressor C1 thereby causing RNA polymerase to
position at PL and PR for lytic growth.

Summary of bacteriophage λ’s circular genome

The proteins excissionase and integrase on the left-hand side of the circular DNA have Pi and att
(attachment site) as their respective promoters. Excisionase (Xis) is a sequence-specific DNA binding
protein required for excisive recombination. Integrase is encoded by the int gene. It is associated with
the lysogenic cycle because in lysogenic growth, we have integration of the phage genome into the host
genome and thus associated with lysogenic cycle. On the right-hand side of the plasmid, we have Q,
lysis protein, head genes and tail genes. These are all associated with lytic growth because in the lytic
cycle, the virus concerns itself with exploiting the host and making new phages. Head genes and tail
genes are thus required to make new phage head and tail.

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