total description of lactose operon, galactose operon, arabinose operon, tryptophan operon and their regulations and mechanisms

1. Operon concepts
D.INDRAJA

2. • The basic concept about how gene regulation occurs at the level of
transcription in bacteria was provided by the classical model called operon
model(formulated by jacob and monad in 1961)
• Operons consist of multiple genes grouped together with a promoter and an
operator.
• Operons are present in prokaryotes (bacteria and archaea), but are absent in
eukaryotes.
Operon Structure
• Operons are regions of DNA that contain clusters of related genes.
• They are made up of a promoter region, an operator, and multiple related
genes.
• The operator can be located either within the promoter or between the
promoter and the genes.
• RNA polymerase initiates transcription by binding to the promoter region.
• The location of the operator is important as its regulation either allows or
prevents transcription of the genes into mRNA.

3. •The product of lac operon is involved in the conversion of the disachharide
sugar lactose in to its monosachharide units glucose and galactose
•Operons can be under negative or positive control. Negative control involves
turning off the operon in the presence of a repressormolecule. The repressor
binds to the operator in such a way that the movement or binding of RNA
polymerase is blocked and transcription cannot proceed.

4. • An inducible operon is one that is usually off. In the absence of an inducer
the operator is blocked by a repressor molecule. When the inducer is present
it interacts with the repressor protein, releasing it from the operator and
allowing transcription to proceed.

5. What makes the lac operon turn on?
• E. coli bacteria can break down lactose, but it's not their favorite fuel. If
glucose is around, they would much rather use that. Glucose requires fewer
steps and less energy to break down than lactose. However, if lactose is the
only sugar available, the E. coli will go right ahead and use it as an energy
source.
• To use lactose, the bacteria must express the lac operon genes, which encode
key enzymes for lactose uptake and metabolism. To be as efficient as
possible, E. coli should express the lac operon only when two conditions are
met:
• Lactose is available, and
• Glucose is not available
• How are levels of lactose and glucose detected, and how how do changes in
levels affect lac operon transcription? Two regulatory proteins are involved:
• One, the lac repressor, acts as a lactose sensor.
• The other, catabolite activator protein (CAP), acts as a glucose sensor.
• These proteins bind to the DNA of the lac operon and regulate its
transcription based on lactose and glucose levels.

6. Structure of the lac operon
• The lac operon contains three genes: lacZ, lacY, and lacA. These
genes are transcribed as a single mRNA, under control of one
promoter.
• Galactoside permease (also known as lactose permease).(lac Y)
 Transports lactose into the cell across the cell membrane.
• Galactosidase(lac Z)  Hydrolyzes lactose to glucose and galactose.
• Thiogalactoside transacetylase(lac A)

7. • In addition to the three genes, the lac operon also contains a number of
regulatory DNA sequences. These are regions of DNA to which particular
regulatory proteins can bind, controlling transcription of the operon.
• The promoter is the binding site for RNA polymerase, the enzyme that
performs transcription.
• The operator is a negative regulatory site bound by the lac repressor
protein. The operator overlaps with the promoter, and when the lac repressor
is bound, RNA polymerase cannot bind to the promoter and start
transcription.
• The CAP binding site is a positive regulatory site that is bound by
catabolite activator protein (CAP). When CAP is bound to this site, it
promotes transcription by helping RNA polymerase bind to the promoter.
The lac repressor
• The lac repressor is a protein that represses (inhibits) transcription of
the lac operon. It does this by binding to the operator, which partially
overlaps with the promoter. When bound, the lac repressor gets in RNA
polymerase's way and keeps it from transcribing the operon.

8. • The gene that encodes the lac repressor is named lacI, and is under control
of its own promoter.
• The lacI gene happens to be found near the lac operon, but it is not a part of
the operon and is expressed separately.
• lacI is continually transcribed, so its protein product – the lac repressor – is
always present.
• When lactose is not available, the lac repressor binds tightly to the operator,
preventing transcription by RNA polymerase. However, when lactose is
present, the lac repressor loses its ability to bind DNA. It floats off the
operator, clearing the way for RNA polymerase to transcribe the operon.

9. The lac inducer
• This change in the lac repressor is caused by the small molecule called
inducer which is a allolactose, an isomer (rearranged version) of lactose.
When lactose is available, some molecules will be converted to allolactose
inside the cell. Allolactose binds to the lac repressor and makes it change
shape so it can no longer bind DNA.
• Allolactose is an example of an inducer, a small molecule that triggers
expression of a gene or operon. The lac operon is considered an inducible
operon because it is usually turned off (repressed), but can be turned on in
the presence of the inducer allolactose.
• Another inducer of the lac operon is isopropylthiogalactoside (IPTG).
Unlike allolactose, this inducer is not metabolized by E. coli and so, is useful
for experimental studies of induction only.
Lac Operon in absence of Inducers
• In the absence of an inducer such as allolactose or IPTG, the lacI gene is
transcribed and the resulting repressor protein binds to the operator site of
the lac operon, Olac, and prevents transcription of the lacZ, lacY and lacA
genes.

11. Catabolite activator protein (CAP)
• RNA polymerase alone does not bind very well to the lac operon promoter.
It might make a few transcripts, but it won't do much more unless it gets
extra help from catabolite activator protein (CAP). CAP binds to a region
of DNA just before the lac operon promoter and helps RNA polymerase
attach to the promoter, driving high levels of transcription.
• CAP isn't always active (able to bind DNA). Instead, it's regulated by a small
molecule called cyclic AMP (cAMP). cAMP is a "hunger signal" made
by E. coli when glucose levels are low. cAMP binds to CAP, changing its
shape and making it able to bind DNA and promote transcription. Without
cAMP, CAP cannot bind DNA and is inactive.
• CAP is only active when glucose levels are low (cAMP levels are high).
Thus, the lac operon can only be transcribed at high levels when glucose is
absent. This strategy ensures that bacteria only turn on the lac operon and
start using lactose after they have used up all of the preferred energy source
(glucose).

12. Lac operon in the presence of Glucose
• When glucose is present, E. coli does not need to use lactose as a
carbon source and so the lac operon does not need to be active.
• Thus the system has evolved to be responsive to glucose.
• Glucose inhibits adenylate cyclase, the enzyme that synthesizes cAMP
from ATP.
• Thus, in the presence of glucose the intracellular level of cAMP falls, so
CRP cannot bind to the lac promoter, and the lac operon is only weakly
active (even in the presence of lactose).
• Lac operon in the absence of Glucose
• When glucose is absent, adenylate cyclase is not inhibited, the level of
intracellular cAMP rises and binds to CRP.
• Therefore, when glucose is absent but lactose is present, the CRP–cAMP
complex stimulates transcription of the lac operon and allows the lactose
to be used as an alternative carbon source.
• In the absence of lactose, the lac repressor, of course, ensures that the lac
operon remains inactive.
• These combined controls ensure that the lacZ, lacY and lacA genes are
transcribed strongly only if glucose is absent and lactose is present.

14. Negative Control of the lac Operon
• The protein that inhibits transcription of the lac operon is a tetramer
with four identical subunits called lac repressor. The lac repressor is
encoded by the lacI gene, located upstream of the lac operon and has
its own promoter. Expression of the lacI gene is not regulated and
very low levels of the lac repressor are continuously synthesized.
Genes whose expression is not regulated are called constitutive genes.
• In the absence of lactose the lac repressor blocks the expression of
the lac operon by binding to the DNA at a site, called the operator that
is downstream of the promoter and upstream of the transcriptional
initiation site. The operator consists of a specific nucleotide sequence
that is recognized by the repressor which binds very tightly, physically
blocking (strangling) the initiation of transcription.

15. Positive and Negative Regulation of Lac Operon
• The lac operon is a good example of the negative control (negative
regulation) of gene expression in that bound repressor prevents transcription
of the structural genes.
• Positive control or regulation of gene expression is when the regulatory
protein binds to DNA and increases the rate of transcription.
• In this case, the regulatory protein is called an activator. The CAP/CRP
involved in regulating the lac operon is a good example of an activator.
• Thus the lac operon is subject to both negative and positive control.
Negative regulation

16. positive regulation
Glucose CAP binds Lactose Repressor binds Transcription
+ – – + No
+ – + – Some
– + – + No
– + + – Yes

17. Diauxic growth curve
• A diauxic growth curve refers to the growth curve generated by
an organism which has two growth peaks. The theory behind the diauxic
growth curve stems from Jacques Monod's Ph.D. research in 1940.
• A simple example involves the bacterium Escherichia coli (E. coli), the best
understood bacterium.
• The bacterium is grown on a growth media containing two types of sugars,
one of which is easier to metabolize than the other (for
example glucose and lactose).

18. • First, the bacterium will metabolize all the glucose, and grow at a higher
speed. Eventually, when all the glucose has been consumed, the bacterium
will begin the process of expressing the genes to metabolize the lactose.
• This will only occur when all glucose in the media has been consumed. For
these reasons, diauxic growth occurs in multiple phases.

21. Structure of galactose operon
• Out side the operon (far from transcription site) GalR is present which
synthesizes repressor molecule for the galactose operon
• The gal operon contains two operators, OE (for external) at -60.5 postion
and OI (for internal) at +53.5 position. These operators bind the
repressor, GalR, which is encoded from outside the operator region. For this
repressor protein to function properly, the operon also contains a histone
binding site( at 6.5 position) to facilitate this process.
• it has two overlapping promoters P1(upper phase) &P2 (lower phase) are
present having transcription sites at +1 &-5 positions

22. • An additional site, known as the activating site, is found following the
external operator, but upstream of P2. This site serves as the binding region
for the cAMP-CRP complex, which modulates the activity of the promoters
and thus, gene expression.
• The galactose operon has 4 structural genes
 galE  UDP galactose 4-epimerase
 galT  galactose -1- phosphate uridylyl transferase
 galK  galactokinase
 galM  mutarotase
 A part from these genes galR  it is a unlinked gene that encodes repressor
for the gal operon
How does the galctose form in the cell?
• Galactose may enter in to the cell by permeases
• β-D-galactose generated from lac operon enzyme β-galactosidase( when lac
operon is on the enzyme galactosidase breaks in to galctose and
galactosidase)

23. It links the enzymes of lactose and galactose
metabolism in to common pathway
GALACTOSE METABOLISM

25. Gal R mediated DNA loop formation/repression

27. • The binding of GalR to OE represses P1 and activates P2
• GalR bound to OE is located on the same DNA face as RNAP bound to P1 ,
but on the opposite DNA face as RNAP bound to P2
• GalR represses P1 by inhibiting the rate determining open complex
formation through RNAP contacts . This mode of repression is termed
“contact inhibition”
• While P1 is repressed by GalR-OE complex, P2 is activated by GalR-OE
complex by a direct contact between GalR and RNAP, “contact activation” .
• GalR-OE enhances open complex formation at P2 where inhibits open
complex formation in P1 so P1 is repressed and P2 is enhanced

30. 4 . Regulation of gal promoters by CAMP CRP complex (CCC)
• Role of CCC The gal operon includes a 16-bp activating site (AS) located at
40.5 that binds the regulator CCC for activating P1 and repressing P2
• The overlapping of the AS at 40.5 with the 35 element of P1 is a feature of
CCC-regulated Class II promoters.
• In contrast, in Class I promoters, the AS is located upstream (61.5) to the
promoter region for RNA polymerase (RNAP).
• CCC represses P2 by decreasing open complex formation of RNAP. In
contrast, CCC activates P1 by increasing both closed complex formation and
isomerization from the closed complex to the open complex of RNAP .
• The AS of CCC is located on the same face as RNAP at P1 and on the
opposite face of RNAP at P2.
• By binding to AS, CCC switches transcription initiation from P2 to P1.
Glucose high  CRP CAMP levels
Glucose low  CRP CAMP levels
(Only when lactose or galactose are
present in the medium)

31. Gal Isorepressor
• The gal operon is also regulated by an isorepressor (GalS). Although GalS
does not seem to repress the gal promoters by DNA looping, the isorepressor
does stimulate P2 and repress P1, the same way that GalR does by binding to
OE, except that the effects are weaker.
• GalR and GalS are 85% similar in their amino acid sequences . By their
homology with proteins (GalR-LacI family) whose structures are known

33. Introduction
• The 20 common amino acids are required in large amount for protein
synthesis, and E.coli can synthesize all of them.
• The genes for the enzymes needed to synthesize a given amino acid are
generally clustered in an operon and are expressed whenever existing
supplies of that amino acid are inadequate for cellular requirements.
• When the amino acid is abundant the biosynthetic enzymes are not needed
and the operon is repressed
• Bacteria such as Escherichia coli (a friendly inhabitant of our gut) need
amino acids to survive—because, like us, they need to build proteins. One of
the amino acids they need is tryptophan.
• If tryptophan is available in the environment, E. coli will take it up and use it
to build proteins. However, E. coli can also make their own tryptophan using
enzymes that are encoded by five genes. These five genes are located next to
each other in what is called the trp operon.
• If tryptophan is present in the environment, then E. coli bacteria don't need
to synthesize it, so transcription of the genes in the trp operon is switched
"off." When tryptophan availability is low, on the other hand, the operon is
switched "on," the genes are transcribed, biosynthetic enzymes are made,
and more tryptophan is produced.

34. Structure of the trp operon
• The trp operon includes five genes that encode enzymes needed for
tryptophan biosynthesis, along with a promoter (RNA polymerase binding
site) and an operator (binding site for a repressor protein).
• The genes of the trp operon are transcribed as a single mRNA.
•The trp operator region partly overlaps the trp promoter.
•The operon is regulated such that transcription occurs when tryptophan in the
cell is in short supply

35. • Structural genes are TrpE, TrpD, TrpC, TrpB and TrpA
1. trpE: It enodes the enzyme Anthranilate synthase I
2. trpD: It encodes the enzyme Anthranilate synthase II
3. trpC: It encodes the enzyme N-5’-Phosphoribosyl anthranilate isomerase and
Indole-3-glycerolphosphate synthase
4. trpB: It encodes the enzyme tryptophan synthase-B sub unit
5. trpA: It encode the enzyme tryptophan synthase-A sub unit
trpE trpD trpC
trpB/trpA
trpC

36. Mechanisms of operon
• Repression
• Attenuation
Repression
Turning the operon "on" and "off“
operator stretch of DNA is recognized by a regulatory protein known as
the trp repressor. When the repressor binds to the DNA of the operator, it
keeps the operon from being transcribed by physically getting in the way of
RNA polymerase, the transcription enzyme.
trp repressor
The trp repressor protein is encoded by a gene called trpR.
This gene is not part of the trp operon, and it's located elsewhere on the
bacterial chromosome, where it has its own promoter and other regulatory
sequences.
Translation mediated
RNA binding protein mediated

37. • The trp repressor does not always bind to DNA.
• Instead, it binds and blocks transcription only when tryptophan is present.
When tryptophan is around, it attaches to the repressor molecules and
changes their shape so they become active.
• A small molecule like trytophan, which switches a repressor into its active
state, is called a corepressor.
COREPRESSOR

38. In the Presence of Tryptophan
•When tryptophan is present, the enzymes for tryptophan biosynthesis are not
needed and so expression of these genes is turned off.
•This is achieved by tryptophan binding to the repressor to activate it so that it
now binds to the operator and stops transcription of the structural genes.
•Binding of repressor protein to operator overlaps the promoter, so RNA
polymerase cannot bind to the prometer. Hence transcription is halted.
•In this role, tryptophan is said to be a co-repressor. This is negative control,
because the bound repressor prevents transcription.

39. In the Absence of Tryptophan
• In the absence of tryptophan, a trp repressor protein encoded by a separate
operon, trpR, is synthesized and forms a dimer.
• However, this is inactive and so is unable to bind to the trp operator and the
structural genes of the trp operon are transcribed.

41. Attenuation
Translation mediated
• A second mechanism, called attenuation, is also used to control expression
of the trp operon.
• The 5′ end of the polycistronic mRNA transcribed from the trp operon has a
leader sequence upstream of the coding region of the trpE structural gene.
• This section lies between the operator and the first gene of the operon and is
called the leader. The leader encodes a short polypeptide and also contains
an attenuator sequence. The attenuator does not encode a polypeptide, but
when transcribed into mRNA, it has self-complementary sections and can
form various hairpin structures.
• This leader sequence encodes a 14 amino acid leader peptide containing
two tryptophan residues.
• The function of the leader sequence is to fine tune expression of the trp
operon based on the availability of tryptophan inside the cell.

42. • The leader sequence contains four regions (numbered 1–4) that can form a
variety of base paired stem-loop (‘hairpin’) secondary structures.
• The regions are: Region 1, region 2, region 3 and Region 4. Region 3 is
complementary to both region 2 and region 4.
• If region 3 and region 4 base pair with each other, they form a loop like
structure called attenuator and it function as transcriptional termination. If
pairing occur between region 3 and region 2, then no such attenuator form so
that transcription continues.

43. What mechanism determines
whether sequence 3 pairs with
sequence 2 or with sequence 4 ?
• When tryptophan concentrations are high,
concentrations of charged tryptophan tRNA are also
high.
• This allows translation to proceed rapidly past the
two trp codons of sequence 1 and into sequence 2,
before sequence 3 is synthesized by RNA
polymerase.
• In this situation, sequence 2 is covered by the
ribosome , and unavailable for paring to sequence 3
when sequence 3 is synthesized; the attenuator
structure sequence 3 and 4 forms and transcription
halts.
• When tryptophan concentrations are low, the
ribosome stalls at the two Trp codons in sequence 1
because the charged tryptophan tRNA is
unavailable. • Sequence 2 remains free while
sequence 3 is synthesized, allowing these two
sequences to base pair and permitting transcription
to proceed.

44. • Attenuation depends on the fact that, in bacteria, ribosomes attach to mRNA
as it is being synthesized and so translation starts even before transcription
of the whole mRNA is complete.
When Trypophan is abundant
• If there is plenty of tryptophan, the ribosome won't have to wait long for a
tryptophan-carrying tRNA, and will rapidly finish the leader polypeptide.
• If the ribosome translates quickly, it will fall off the mRNA after translating
the leader peptide. This allows the terminator hairpin and an associated
hairpin to form, making RNA polymerase detach and ending transcription.
• When tryptophan is abundant, ribosomes bind to the trp polycistronic
mRNA that is being transcribed and begin to translate the leader sequence.
• Now, the two trp codons for the leader peptide lie within sequence 1, and the
translational Stop codon lies between sequence 1 and 2.
• During translation, the ribosomes follow very closely behind the RNA
polymerase and synthesize the leader peptide, with translation stopping
eventually between sequences 1 and 2.
• At this point, the position of the ribosome prevents sequence 2 from
interacting with sequence 3.
• Instead sequence 3 base pairs with sequence 4 to form a 3:4 stem loop which
acts as a transcription terminator.
• Therefore, when tryptophan is present, further transcription of the trp operon
is prevented.

46. When Tryptophan is scarce
• If there is little tryptophan, the ribosome will stall at the Trp
codons (waiting for a Trp-carrying tRNA) and will be slow to
finish translation of the leader.
• If the ribosome translates slowly, it will pause, and its pausing
causes formation of the antiterminator (non-terminating hairpin).
This hairpin prevents formation of the terminator and allows
transcription to continue.
• If, however, tryptophan is in short supply, the ribosome will pause
at the two trp codons contained within sequence 1.
• This leaves sequence 2 free to base pair with sequence 3 to form a
2:3 structure (also called the anti-terminator), so the 3:4 structure
cannot form and transcription continues to the end of the trp
operon.
• Hence the availability of tryptophan controls whether transcription
of this operon will stop early (attenuation) or continue to
synthesize a complete polycistronic mRNA.

48. Conclusion
• This mechanism may be complex, but the result is pretty straightforward.
• When tryptophan is abundant the ribosome moves quickly along the
leader, the terminator hairpin forms, and transcription of the trp operon ends.
• When tryptophan is scarce  the ribosome moves slowly along the leader,
the anti-terminator hairpin forms, and transcription of the trp operon
continues.
• In other words, the logic of attenuation is the same as that of regulation by
the trp repressor.
• In both cases, high levels of tryptophan in the cell shut down the expression
of the operon. This makes sense, since high levels of tryptophan mean that
the cell does not need to make more biosynthetic enzymes to produce
additional tryptophan.
RNA binding protein mediated
• In B.subtilis transcriptional attenuation of trp operon is mediated by RNA
binding terminator protein called TRAP(Trp-binding A ttenuation Protein)
• TRAP forms a multimer of 11 subunits and each subunit binds a single
tryptophan amino acid .TRAP is activated by binding to the amino acid
tryptophan
• TRAP bind to a sequence in the leader segment of transcript. Binding of
TRAP causes the formation of termination hairpin. The termination of
transcription then prevents the production of the tryptophan biosynthetic
enzymes

49. • In the absence of tryptophan, TRAP doesnot bind and the mRNA adopts a
structure that prevents the terminator hairpin from forming.
• Protein anti-TRAP controls the activity of TRAP, which binds to TRAP, and
prevents it from repressing the tryptophan operon

50. ARABINOSE OPERON

51. • The L-arabinose operon, also called the ara or araBAD operon, is
an operon required for the breakdown of the five-carbon sugar L-
arabinose in Escherichia coli.
• Arabinose is another non-glucose carbohydrate source, for which bacterial
cells have genetic capabilities for utilizing it as an alternative source of
carbon.
• For utilization of Arabinose several genes operate. Few genes are required
for its transport into the cell. Another set of gene products is required for the
conversion of Arabinose into Xylulose.
• Then another set of enzymes is required for converting Xylulose into
Fructose1,6-di phosphate, which becomes the part of glycolytic pathway.
(pentose phosphate pathway)
• Multiple gene metabolic pathway is regulated by a common protein
complex; so it is called ‘Arabinose Regulon’.
• It is a Complex regulatory system
• First studied by Ellis Englesberg
• Arabinose operon can be regulated both positively and negatively
• Exhibits catabolite repression

52. Structure
• L-arabinose operon is composed of structural genes and regulatory regions
including the operator region (araO1, araO2) and the inducer region
(araI1, araI2).
• The structural genes, araB, araA and araD, encode enzymes for L-
arabinose catabolism.
• There is also a CAP binding site where CAP-cAMP complex binds to and
facilitates catabolite repression, and results in positive regulation of ara
BAD when the cell is starved of glucose

53. • The regulatory gene, araC, is located upstream of the L-arabinose operon
and encodes the arabinose-responsive regulatory protein AraC.
• Both ara C and ara BAD have a discrete promoter where RNA
polymerase binds and initiates transcription.
• araBAD and araC are transcribed in opposite directions from
the araBAD promoter (PBAD) and araC promoter (PC) respectively
Structural genes
• araA  L-arabinose isomerase which catalyses isomerization between L-
arabinose and L-ribulose
• araB  ribulokinase which catalyses phosphorylation of L-ribulose to
form L-ribulose-5-phosphate.
• araD  L-ribulose-5-phosphate 4-epimerase, which
catalyses epimerization between L-ribulose 5-phosphate and D-xylulose-5-
phosphate

54. Regulation
• The araC gene is adjacent to the ara operon
• It has its own promoter, It encodes a regulatory protein, AraC
• AraC can bind to three different operator sites ,Designated araI, araO1 and
araO2
• When araC protein is depleted, the ara C gene is transcribed from its own
promoter
• The AraC protein can act as either a negative or positive regulator of
transcription Depending on whether or not arabinose is present

55. • AraC functions as a homodimer, which can control transcription
of araBAD through interaction with the operator and the initiator region on
L-arabinose operon.
• Each AraC monomer is composed of two domains including a DNA binding
domain and a dimerisation domain.
• The dimerisation domain is responsible for arabinose-binding.
• AraC undergoes conformational change upon arabinose-binding, in which,
it has two distinct conformations.The conformation is purely determined by
the binding of allosteric inducer arabinose

56. Negative regulation of araBAD
• When arabinose is absent, cells do not need the araBAD products for breaking
down arabinose.
• Therefore, dimeric AraC acts as a repressor: one monomer binds to the
operator of the araBAD gene (araO2), another monomer binds to a
distant DNA half site known as araI.
• This leads to the formation of a DNA loop. This orientation blocks RNA
polymerase from binding to the araBAD promoter.
• Therefore, transcription of structural gene araBAD is inhibited.

57. Positive regulation of araBAD
• Expression of the araBAD operon is activated in the absence of glucose and
in the presence of arabinose.
• When arabinose is present, both AraC and CAP work together and function
as activators.
Via AraC
• AraC acts as an activator in the presence of arabinose.
• AraC undergoes a conformational change when arabinose binds to the
dimerization domain of AraC. As a result, the AraC-arabinose complex falls
off from araO2 and breaks the DNA loop.
• Hence, it is more energetically favourable for AraC-arabinose to bind to two
adjacent DNA half sites: araI1 and araI2 in the presence of arabinose.
• One of the monomers binds araI1, the remaining monomer binds araI2 - in
other words, binding of AraC to araI2 is allosterically induced by arabinose.
• One of the AraC monomers places near to the araBAD promoter in this
configuration, which helps to recruit RNA polymerase to the promoter to
initiate transcription

58. CAP/cAMp
• CAP act as a transcriptional activator only in the absence of E. coli's
preferred sugar, glucose.
• When glucose is absent, high level of CAP protein/cAMP complex bind to
CAP binding site, a site between araI1 and araO1.
• Binding of CAP/cAMP is responsible for opening up the DNA loop
between araI1 and araO2, increasing the binding affinity of AraC protein
for araI2 and thereby promoting RNA polymerase to bind
to araBAD promoter to switch on the expression of the araBAD required for
metabolising L-arabinose.

59. Autoregulation of AraC
• The expression of araC is negatively regulated by its own protein product,
AraC.
• The excess AraC binds to the operator of the araC gene, araO1, at high
AraC levels, which physically blocks the RNA polymerase from accessing
the araC promoter.
• Therefore, the AraC protein inhibits its own expression at high
concentrations

60. Mutations in the arabinose operon
• A mutation in the araA gene will cause the bacterial cell to become
arabinose negative. Bacteria no longer uses arabinose as carbon source.
• araB gene mutation results the same.
• araD gene mutation results in cell death.
• Mutation of araC gene causes the promoters (pBAD) and pC to become
inactive, permanently repressed.
Similarities between lactose- and arabinose-operon:
• Both of them contains three structural genes. • Inducible
• When glucose is present at high levels it prevents both the synthesis of
arabinose and lactose.
• The function of both the operons are parallel. they undergo positive and
negative regulation
• The products formed in both the operons are similar,
• positive regulation : sugars are formed
• negative regulation : no sugar