Chapter 15:
Regulation of Gene Expression
Anablep anablep with its “4 eyes”. Upper half
of lids look aerially while the lower half looks
into the water.
Cells of the two parts of the eye exhibit
differential gene expression
• Individual bacteria respond to environmental change
by regulating their gene expression
• Express only genes whose products may be needed
presently by the cell. (Don’t want to waste energy)
• E. coli lives in the human colon & can fine-tune its metabolism
to the changing environment and food sources
– If tryptohan is lacking, the cell responds by activating a
gene that starts a metabolic pathway to produce
tryptophan from another food source that is present.
– If tryptophan is plentiful, the bacteria stop making
tryptophan to conserve energy.
• This metabolic control occurs on two levels
1. Adjusting the activity of enzymes already present. Sensitivity to chemical
clues
When there is a build up of tryptophan, it shuts off the production of Enzyme 1
Short term response
2.
Regulating the genes encoding the metabolic enzymes
• Tryptophan can shut down the transcription of a gene is a longer term response
(a) Regulation of enzyme
activity
Feedback
inhibition
(b) Regulation of enzyme
production
Precursor
Enzyme 1
Enzyme 2
Enzyme 3
Gene 1
Gene 2
Regulation
of gene
expression
Gene 3
–
Enzyme 4
Gene 4
–
Enzyme 5
Tryptophan
Figure 18.20a, b
Gene 5
Operons: The Basic Concept
 In bacteria, genes are often clustered into groups of
genes (such as the 5 for tryptophan) called operons,
composed of:
1.
2.
An operator, an “on-off” switch which is a segment of DNA that lies
between promoter and enzyme-coding genes
A promoter – 1 for the entire operon
3.
Genes for metabolic enzymes
Animation
• The Trp operon
– Is usually turned “On” (with no repressor protein stopping transcription)
– Can be switched off by a protein called a repressor protein
• trpR is a regulatory gene which is continually expressed in small amounts. It
produces the repressor protein that binds to Operator to prevent transcription
trp operon
Promoter
DNA
Promoter
Genes of operon
trpD
trpC
trpE
trpR
Regulatory
gene
mRNA
5
3
Operator
Start codon
RNA
polymerase mRNA 5
Inactive
repressor
(a) Tryptophan absent, repressor inactive, operon on.
RNA polymerase attaches to the DNA at the
promoter and transcribes the operon’s genes.
Figure 18.21a
trpA
Stop codon
E
Protein
trpB
D
C
B
A
Polypeptides that make up
enzymes for tryptophan synthesis
Animation
Operator
DNA
trpR
No RNA made
Regulatory
gene
RNA
polymerase
mRNA
Inactive
repressor
Active
repressor
Protein
Tryptophan
(corepressor)
(b)
Tryptophan present, repressor active, operon off.
As tryptophan accumulates, it inhibits its own production by
activating the repressor protein. Tryptophan as a a corepressor
Repressible and Inducible Operons: Two
Types of Negative Gene Regulation
• In a repressible operon
– Transcription is usually on but can be repressed when small
amount of Tryptophan binds to allosterically to regulatory
protein
– Binding of a specific repressor protein to the operator shuts off
transcription
– Trp operon
• In an inducible operon
– Induced by a chemical signal (Allolactose in lac operon)
– Binding of an inducer to an innately inactive repressor
inactivates the repressor and turns on transcription
• The lac operon: regulated synthesis of Inducible enzymes.
• Regulates the catabolism of lactose to galactose and glucose
• Needs an inducer to remove repressor and start transcription
• animation
Promoter
Regulatory
gene
DNA
Operator
lacl
lacZ
3
mRNA
No
RNA
made
RNA
polymerase
5
Active
Protein
repressor
Lactose absent, repressor active, operon off.
(a)
The lac repressor is innately active, and in the absence of lactose it switches
off the
operon by binding to the operator.
Figure
18.22a
lac operon
DNA
lacl
lacz
3
mRNA
5
(b)
lacA
RNA
polymerase
mRNA 5'
5
mRNA
-Galactosidase
Protein
Allolactose
(inducer)
lacY
Permease
Transacetylase
Inactive
repressor
When Lactose is present, the repressor is inactive, operon is on & β –galactosidase is
produced.
Allolactose, an isomer of lactose, acts as the inducer by derepresses the operon by
inactivating the repressor.
In this way, the enzymes for lactose utilization are induced.
a. No lactose present, no need to
produce enzymes to hydrolyze
lactose to glucose & galactose
b. If Lactose is present, operon
needs to be turned on.
Allolactose (inducer) binds to
repressor, changes its shape
making it drop off leaving RNA
polymerase to start
transcription
• Inducible enzymes
– Usually function in catabolic pathways
– Lactose broken down into glucose and galactose
– lac operon to produce B - galactosidase
• Repressible enzymes
– Usually function in anabolic pathways
– Tryptophan being produced
– trp operon to produce tryptophan
• Regulation of both the trp and lac operons
– Involves the negative control of genes, because the
operons are switched off by the active form of the
repressor protein
Positive Gene Regulation
• If Lactose is present and glucose is lacking, E. coli will break down lactose
for energy but how does it sense that glucose is lacking?
• It senses this through an allosteric regulatory protein called Catabolite
Activator Protein (CAP) that binds to a small molecule called cyclic AMP
(cAMP)
• CAP acts as an activator to bind to DNA to stimulate transcription of a
gene (such as the lac operon)
• Think of it like cAMP pushing CAP to make RNA polymerase go faster to
make the enzymes to break lactose down to glucose
• In E. coli, when glucose, (a preferred food source), is scarce, cAMP
(cyclic AMP) builds up
– the lac operon is activated by the binding of a regulatory protein,
catabolite activator protein (CAP) activated by the binding of
cAMP to CAP changing its conformation. Thus allowing
transcription
– cAMP is the green light that tells CAP to floor it!
Promoter
DNA
lacl
lacZ
RNA
Operator
polymerase
can bind
and transcribe
CAP-binding site
cAMP
Active
CAP
Inactive
CAP
(a)
Inactive lac
repressor
Lactose present, glucose scarce (cAMP level high): abundant lac mRNA synthesized.
If glucose is scarce, the high level of cAMP activates CAP, and the lac operon produces large
amounts of mRNA for the lactose pathway.
• When glucose levels in an E. coli cell increases (& lactose levels are
low) there is a decrease in cAMP. CAP detaches from the lac
operon due to the release of cAMP to CAP changing its
conformation, & turning it off
• Animation
Promoter
DNA
lacl
lacZ
CAP-binding site
Operator
RNA
polymerase
can’t bind
Inactive
CAP
Inactive lac
repressor
Lactose present, glucose present (cAMP level low): little lac mRNA synthesized.
When glucose is present, cAMP is scarce, and CAP is unable to stimulate transcription.
Figure 18.23b
(b)
Eukaryotic gene expression is regulated at many stages
• All organisms must
regulate which genes
are expressed at any
given time. Which
ones are turned on or
off.
• In multicellular
organisms regulation
of gene expression is
essential for cell
specialization
• ~20% of protein coding
genes are being
expressed at any time
in human cells
Differential Gene Expression
• Almost all the cells in an organism are genetically
identical with the exception of gametes
• Differences between cell types result from differential
gene expression, the expression of different genes by
cells with the same genome
– RBC from an epithelial cell to a nerve cells
• Abnormalities in gene expression can lead to diseases
including cancer
• Gene expression is regulated at many stages
Signal
Stages in gene
expression that can
be regulated in
eukaryotic cells.
NUCLEUS
Chromatin
Chromatin modification:
DNA unpacking involving
histone acetylation and
DNA demethylation
DNA
Gene available
for transcription
Gene
Transcription
RNA
Exon
Primary transcript
Intron
RNA processing
Cap
Tail
mRNA in nucleus
Transport to cytoplasm
CYTOPLASM
mRNA in cytoplasm
Degradation
of mRNA
Translation
Polypeptide
Protein processing, such
as cleavage and
chemical modification
Degradation
of protein
Active protein
Transport to cellular
destination
Cellular function (such
as enzymatic activity,
structural support)
Signal
NUCLEUS
Chromatin
Chromatin modification:
DNA unpacking involving
histone acetylation and
DNA demethylation
DNA
Gene available
for transcription
Gene
Transcription
RNA
Exon
Primary transcript
Intron
RNA processing
Cap
Tail
mRNA in nucleus
Transport to cytoplasm
CYTOPLASM
Figure 18.6b
CYTOPLASM
mRNA in cytoplasm
Degradation
of mRNA
Translation
Polypeptide
Protein processing, such
as cleavage and
chemical modification
Degradation
of protein
Active protein
Transport to cellular
destination
Cellular function (such
as enzymatic activity,
structural support)
Regulation of Chromatin Structure
• The genes within highly packed heterochromatin
(DNA + proteins) are usually not expressed
– Euchromatin is found in eukaryotes. Less compacted DNA
• Chemical modifications to histones and DNA of
chromatin influence both chromatin structure and
gene expression
• Acetylation- allows transcription
• Methylation – blocks transcription
• Phosphorylation – promotes
transcription
Histone Modifications
For the Transcription of a gene on DNA to occur, histones must be
modified to uncoil the DNA to allow for transcription
• In histone acetylation, acetyl groups (-COCH3) are attached to
positively charged lysines in histone tails
– Histone tails no longer will bind to adjacent nucleosomes
– This loosens chromatin structure, thereby promotes the
initiation of transcription
– Histone acetylation enzymes may
promote the initiation of transcription.
Kosigrin animation
Histone
tails
Amino acids
available
for chemical
modification
DNA
double
helix
Nucleosome
(end view)
(a) Histone tails protrude outward from a nucleosome
Acetylated histones
Unacetylated histones
(b) Acetylation of histone tails promotes loose chromatin
structure that permits transcription
• The addition of
methyl groups –
CH3 to Cystosine
(methylation) to
histone tails
promotes
condensing of
chromatin.
– So this turns off
genes
• The addition of
phosphate groups
(phosphorylation)
next to a
methylated amino
acid can loosen
chromatin
– Turns on genes
DNA Methylation
• DNA methylation, the addition of methyl groups to
certain bases in DNA, is associated with reduced
transcription in some species
• DNA methylation can cause long-term inactivation of
genes in cellular differentiation
– Such as in X inactivation when the X chromosomes become
methylated
– Unexpressed genes are more heavily methylated than active
genes.
– Causes suppression of cancer suppressor genes (p53)
Epigenetic Inheritance
• Although the chromatin modifications do not alter DNA
sequence, they may be passed to future generations of cells
• The inheritance of traits transmitted by mechanisms not
directly involving the nucleotide sequence is called epigenetic
inheritance
• Caused by DNA methylation and therefore certain enzymes are
not produced which may be necessary for cell function
• May be the cause of some cancers
• Ghosts in Your Genes
• Epigenetics video
Control & Organization of a Typical
Eukaryotic Gene
• Chromatin-modifying enzymes provide initial control
of gene expression by making a region of DNA either
more or less able to bind the transcription machinery
• Associated with most eukaryotic genes are multiple
control elements, segments of noncoding DNA that
serve as binding sites for transcription factors that
help regulate transcription
• Control elements and the transcription factors they
bind to are critical to the precise regulation of gene
expression in different cell types
A eukaryotic gene and its transcript.
DNA
Enhancer
(distal control
elements)
Upstream
Proximal
control
Transcription
elements start site
Exon
Promoter
Intron
Exon
Poly-A
signal
sequence
Intron Exon
Transcription
termination
region
Downstream
A eukaryotic gene and its transcript.
Enhancer
(distal control
elements)
Proximal
control
elements
Transcription
start site
Exon
DNA
Upstream
Intron
Promoter
Primary RNA
transcript
(pre-mRNA)
Transcription
Exon
5
Exon
Poly-A
signal
sequence
Intron Exon
Intron
Exon
Intron
Transcription
termination
region
Downstream
Poly-A
signal
Exon
Cleaved
3 end of
primary
transcript
A eukaryotic gene and its transcript.
Enhancer
(distal control
elements)
Proximal
control
elements
Transcription
start site
Exon
DNA
Upstream
Transcription
termination
region
Intron
Exon
Intron
Downstream
Poly-A
signal
Intron Exon
Exon
Cleaved
3 end of
primary
RNA processing
transcript
Promoter
Primary RNA
transcript
(pre-mRNA)
Poly-A
signal
sequence
Intron Exon
Transcription
Exon
5
Intron RNA
Coding segment
mRNA
G
P
P
5 Cap
AAA AAA
P
5 UTR
Start
codon
Stop
codon
3 UTR
Poly-A
tail
3
The Roles of Transcription Factors
• To initiate transcription, eukaryotic RNA polymerase
requires the assistance of proteins called transcription
factors
• General transcription factors are essential for the
transcription of all protein-coding genes
• In eukaryotes, high levels of transcription of particular
genes depend on control elements interacting with
specific transcription factors
Enhancers and Specific Transcription Factors
• Proximal control elements are located close to the
promoter
• Distal control elements, groupings of which are called
enhancers, may be far away from a gene or even
located in an intron
– These control elements could be thousands of base pairs
away from the gene on the DNA strand
• An activator is a protein that binds to an enhancer
on the control factor and stimulates transcription of a
gene. Think of it like the key that gets transcription
going
• Activators have two domains, one that binds to DNA
and a second that activates transcription
• Bound activators facilitate a sequence of proteinprotein interactions that result in transcription of a
given gene
McGraw Hill animation
• Some transcription factors function as repressors,
inhibiting expression of a particular gene by a variety
of methods
• Some activators and repressors act indirectly by
influencing chromatin structure to promote or silence
transcription
Activators
Promoter
DNA
Enhancer
Distal control
element
Gene
TATA box
A model for the action of enhancers and transcription activators
Promoter
Activators
DNA
Enhancer
Distal control
element
Gene
TATA box
General
transcription
factors
DNAbending
protein
Group of mediator proteins
A model for the action of enhancers and transcription activators
Promoter
Activators
DNA
Enhancer
Distal control
element
Gene
TATA box
General
transcription
factors
DNAbending
protein
Group of mediator proteins
RNA
polymerase II
Animation
RNA
polymerase II
Transcription
RNA synthesis
initiation complex
A model for the action of enhancers and transcription activators
Enhancer
Control
elements
Promoter
Albumin gene
Cell type–specific transcription
Crystallin
gene
LENS CELL
NUCLEUS
LIVER CELL
NUCLEUS
Available
activators
Available
activators
Albumin gene
not expressed
Albumin gene
expressed
Crystallin gene
not expressed
(a) Liver cell
Crystallin gene
expressed
(b) Lens cell
Enhancer
Control
elements
Promoter
LIVER CELL
NUCLEUS
Albumin gene
Crystallin
gene
Available
activators
Albumin gene
expressed
Crystallin gene
not expressed
Cell type–specific transcription
(a) Liver cell
Enhancer
Control
elements
Promoter
LENS CELL
NUCLEUS
Albumin gene
Crystallin
gene
Available
activators
Albumin gene
not expressed
Crystallin gene
expressed
Cell type–specific transcription
(b) Lens cell
Coordinately Controlled Genes in
Eukaryotes
• Unlike the genes of a prokaryotic operon, each of the
co-expressed eukaryotic genes has a promoter and
control elements
• These genes can be scattered over different
chromosomes, but each has the same combination of
control elements
• Copies of the activators recognize specific control
elements and promote simultaneous transcription of
the genes
Mechanisms of Post-Transcriptional
Regulation
• Transcription alone does not account for gene
expression
• Regulatory mechanisms can operate at various stages
after transcription
• Such mechanisms allow a cell to fine-tune gene
expression rapidly in response to environmental
changes
RNA Processing
• In alternative RNA splicing, different mRNA molecules
are produced from the same primary transcript,
depending on which RNA segments are treated as
exons and which as introns
Exons
DNA
1
3
2
4
5
4
5
Troponin T gene
Primary
RNA
transcript
3
2
1
RNA splicing
mRNA
1
2
3
5
or
1
2
4
5
Initiation of Translation
• The initiation of translation of selected
mRNAs can be blocked by regulatory proteins that
bind to sequences or structures of the mRNA
• Alternatively, translation of all mRNAs
in a cell may be regulated simultaneously
• For example, translation initiation factors are
simultaneously activated in an egg following
fertilization
Protein Processing and Degradation
• After translation, various types of protein processing,
including
– cleavage (such as with pro-insulin which needs to be altered
to become active insulin)
– the addition of chemical groups, are subject to control
(phosphorylation)
– Chemical modifications by the addition/removal of
phosphate groups.
– Functional length (of time) is regulator so that the protein is
only present while it is needed (such as with cyclin).
– To mark a protein for destruction, ubiquitin is added to it.
Chromatin modification
• Genes in highly compacted
chromatin are generally not
transcribed.
• Histone acetylation seems
to loosen chromatin structure,
enhancing transcription.
• DNA methylation generally
reduces transcription.
Transcription
• Regulation of transcription initiation:
DNA control elements in enhancers bind
specific transcription factors.
Bending of the DNA enables activators to
contact proteins at the promoter, initiating
transcription.
• Coordinate regulation:
Enhancer for
Enhancer for
lens-specific genes
liver-specific genes
Chromatin modification
Transcription
RNA processing
RNA processing
• Alternative RNA splicing:
Primary RNA
transcript
mRNA
degradation
Translation
mRNA
Protein processing
and degradation
or
Chromatin modification
Transcription
RNA processing
mRNA
degradation
Translation
Protein processing
and degradation
Translation
• Initiation of translation can be controlled
via regulation of initiation factors.
mRNA degradation
• Each mRNA has a
characteristic life span,
determined in part by
sequences in the 5 and
3 UTRs.
Protein processing and degradation
• Protein processing and
degradation by proteasomes
are subject to regulation.