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Chapter
16
Regulation of Gene
Expression in
Prokaryotes
Lecture Presentation by
Dr. Cindy Malone,
California State University Northridge
© 2015 Pearson Education, Inc.
Section 16.1: Prokaryote Gene Regulation
 E. coli gene regulation has been studied
extensively
– Highly efficient genetic mechanisms have evolved
that turn transcription of specific genes on and off
depending on metabolic need for gene products
– Respond to changes in environment
– Regulate gene activity – replication,
recombination, DNA repair, cell division
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Section 16.1: Inducible and Constitutive
Enzymes
 Inducible enzymes
– Bacteria adapt to environment by producing
inducible enzymes only when specific substrates
are present
 Constitutive enzymes
– Enzymes are continuously produced regardless of
chemical makeup of environment
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Section 16.1: Repressible System
 Repressible system
– Presence of specific molecule inhibits gene
expression
– Abundance of end product in environment
represses gene expression
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Section 16.1: Positive and Negative Control
 Regulation of inducible or repressible type
system under positive control or negative
control
– Negative control: Genetic expression occurs
unless shut off by regulator molecule
– Positive control: Transcription occurs only when
regulator molecule directly stimulates RNA
production
 Either type of system, or both combined, can
induce or repress systems
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16.2 Lactose Metabolism in E. coli Is
Regulated by an Inducible System
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Section 16.2: Lactose Metabolism
 Lactose: Galactose and glucose containing
disaccharide
– In prokaryotes, gene activity is repressed when
lactose is absent and induced when available
– In the presence of lactose, the concentration of
enzymes responsible for its metabolism increases
 inducible enzymes
 Lactose is inducer
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Figure 16-1
Section 16.2: Regulatory Regions
 Transcription is under control of single
regulatory region
– In prokaryotes, genes coding for enzymes with
regulatory functions are organized in clusters
– Regulatory regions usually located upstream of
gene cluster they control
– Regulatory region on same strand  cis-acting
– Trans-acting elements: Molecules that bind cisacting sites
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Section 16.2: Cis- and Trans-Acting Sites
 Cis- and trans-acting sites
– Regulatory site events determine if genes are
transcribed into mRNA
– Binding of trans-acting element at cis-acting site
regulates genes cluster negatively or positively
 Negatively by turning off transcription
 Positively by turning on transcription
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Section 16.2: Lac Operon
 Lac (lactose) operon
– Has three structural genes (genes coding for
primary structure enzyme): lacZ, lacY, and lacA
– Operon has upstream regulatory region consisting
of operator and promoter
(Figure 16-1)
 Entire gene cluster functions to provide rapid
response to presence or absence of lactose
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Figure 16-1
Section 16.2: lacZ and -galactosidase
 lacZ
– Encodes -galactosidase, an enzyme that
converts disaccharide lactose to
monosaccharides glucose and galactose
– Conversion is necessary for lactose to serve as
primary energy source in glycolysis
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Section 16.2: lacY and lacA
 lacY
– Specifies primary structure of permease, an
enzyme that facilitates entry of lactose into
bacterial cell
 lacA
– Encodes enzyme transacetylase, which may be
involved in removal of toxic by-products of lactose
digestion from the cell
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Section 16.2: Lac Operon Structural Genes
 Lac operon structural genes – lacZ, lacY, and
lacA
– All three are transcribed as single unit
– Results in polycistronic mRNA (Figure 16-3)
– Cistron: Part of nucleotide sequence coding for
single gene
– Single mRNA is translated into three gene
products
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Figure 16-3
Section 16.2: LacI Repressor Gene
 Constitutive mutation lacI gene
– Located close to but not part of lac operon
structural genes
– Produces repressor molecule, which regulates
transcription of structural genes
– Allosteric repressor
 Interacts reversibly with another molecule
 Causes conformational change in three-dimensional
shape and change in chemical activity
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Section 16.2: Negative Control
 Lac operon: Negative control
– Operon subject to negative control: Transcription
occurs only when repressor fails to bind
operator region
(Figure 16-5)
– Repressor normally binds DNA sequence in
operator region
 Inhibits RNA polymerase
 Represses transcription of structural genes
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Figure 16-5
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Figure 16-5a
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Figure 16-5b
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Figure 16-5c
Section 16.2: Summary of Operon Model
 Summary of operon model
– series of molecular interactions between proteins,
inducers, and DNA
– No lactose: Enzymes are not needed and
expression of genes encoding enzymes is
repressed
– Lactose present: Indirectly induces activation
of genes by binding repressor
– All lactose metabolized: None is available to bind
to repressor and transcription is repressed
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16.3 The Catabolite-Activating Protein (CAP)
Exerts Positive Control over the lac Operon
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Section 16.3: CAP
 CAP: Catabolite-activating protein
– Exerts positive control over lac operon
– Diminishes expression of operon when glucose
present (catabolite repression)
– Binds to CAP-binding site, facilitating RNA
polymerase binding at promoter and facilitating
transcription
(Figure 16-8)
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Section 16.3: Transcription Levels
 Maximum transcription of structural genes
– Repressor must be bound by lactose
 Does not repress operon expression
– CAP must be bound to CAP-binding site
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Figure 16-8
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Figure 16-8a
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Figure 16-8b
Section 16.3: Glucose Inhibits CAP Binding
 cAMP: Cyclic adenosine monophosphate
– To bind to promoter, CAP must be bound to
cyclic adenosine monophosphate (cAMP)
– Glucose inhibits activity of adenylyl cyclase,
which catalyzes conversion of ATP to cAMP
– Prevents CAP from binding when glucose is
present
(Figure 16-9 and Figure 16-8)
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Figure 16-8
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Figure 16-9
16.4 Crystal Structure Analysis of Repressor
Complexes Has Confirmed
the Operon Model
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Section 16.4: Lac Operon Regulatory Regions
 Lac operon and regulatory regions
– Detailed structure of lac operon and its regulatory
regions reveals three sites for repressor binding
(Figure 16-10)
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© 2015 Pearson Education, Inc.
Figure 16-10
Section 16.4: Crystal Structure Analysis
 Crystal structure analysis
– Determination of the crystal structure of lac
repressor, repressor bound to inducer and
operator DNA
– Genetic and biochemical data complement
missing structural interpretation
 In vivo, all three operators must be bound for
maximum repression
(Figure 16-11a, b)
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Figure 16-11
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Figure 16-11a
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Figure 16-11b
Section 16.4: Repression Loop
 Repression loop
– Binding of repressor to operators O1 and O3
creates repression loop
– Prevents access of RNA polymerase to promoter
(Figure 16-11c)
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© 2015 Pearson Education, Inc.
Figure 16-11c
16.5 The Tryptophan (trp) Operon in
E. coli Is a Repressible Gene System
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Section 16.5: Tryptophan (trp) Operon
 Tryptophan (trp) operon
– Repressible gene system in E. coli
– Wild-type E. coli produce enzymes for
biosynthesis of amino acids and essential
macromolecules
– Tryptophan present: Enzymes necessary for
synthesis of tryptophan are not produced
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Section 16.5: Structural Genes of trp Operon
Structural genes of trp operon
 Five contiguous structural genes transcribed as
polycistronic message
– Involved in tryptophan production
 trpE, D, C, B, A
– Enzymes catalyze biosynthesis of tryptophan
(Figure 16-12)
 trpP: promoter – binding site for RNA Pol
 trpO: operator – binds repressor
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Figure 16-12
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Figure 16-12a
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Figure 16-12b
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Figure 16-12c
16.6 Alterations to RNA Secondary Structure
Contribute to Prokaryotic Gene Regulation
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Section 16.6: Regulation by RNA’s Structure –
Attenuation
 RNA’s secondary structure provides
regulation: Attenuation and riboswitches
– Attenuation: trp structural genes are preceded by
leader sequence containing regulatory site called
an attenuator
– Transcription of leader region occurs even when
operon is repressed in presence of tryptophan
(attenuation)
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Section 16.6: Attenuation: Hairpins
mRNA has potential to fold into two different
stem-loops (hairpins)
 Antiterminator hairpin: In absence of
tryptophan
 Terminator hairpin: In presence of tryptophan
(Figure 16-13)
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© 2015 Pearson Education, Inc.
Figure 16-13
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Figure 16-13a
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Figure 16-13b
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Figure 16-13c
Section 16.6: Attenuation Mechanism
 Leader region
– Contains two tryptophan codons
 Antiterminator hairpin structure
– Forms in absence of tryptophan; ribosome stalls
at codons
 Terminator hairpin
– Forms in presence of tryptophan; ribosome
proceeds through sequence
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16.7 The ara Operon Is Controlled by a
Regulator Protein That Exerts Both Positive
and Negative Control
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Section 16.7: Arabinose Operon
 Arabinose (ara) operon
– Inducible operon analyzed in E. coli
– Positive and negative regulation by AraC protein
– Metabolism of arabinose (sugar) governed by
enzymatic products of three structural genes,
araB, A, and D
(Figure 16-15a)
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© 2015 Pearson Education, Inc.
Figure 16-15a
Section 16.7: AraC Protein
 AraC protein
– System is induced when I region is the only region
bound by AraC
– Transcription controlled by regulatory protein
AraC, which interacts with two regulatory regions:
araI and araO2
– In the presence of arabinose:
 AraC binds to araI and CAP–cAMP to induce
expression
– In the absence of arabinose and CAP–cAMP:
 AraC binds to both araI and araO2; forms loop and
causes repression (Figure 16-15)
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Figure 16-15
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Figure 16-15b
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Figure 16-15c