Control of Gene Expression
Chapter 16
replication (mutation!)
genes
Nucleic acids ~
“software”
DNA
(nucleotides)
transcription
messages
RNA
(nucleotides)
nucleus
ribosome
(cytoplasm)
translation
Protein
(amino acids)
“hardware”
2
3
4
Fig. 16.1
5
Helix-Turn-Helix Motif
6
Homeodomain Motif
7
Zinc Finger Motif
8
Leucine Zipper Motif
9
10
lactose
The Lac Operon:
repressor
repressor
LacI
promoter
operator
LacZ
LacY
LacA
DNA
RNA-P
mRNA
primary RNA
transcript
start codon
stop codon
stop codon
stop codon
protein products of the operon:
betapermease acetylase
galactosidase
11
genotype
phenotype for: Data of Jacob and Monod, 1961
B-gal
Permease
+IPTG
--IPTG
+IPTG
--IPTG
lacI+ Z+ Y+
+
--
+
--
Lac+
lacIc Z+ Y+
+
-+
+
+
-+
--
+
-+
+
+
-+
--
Lacc
LacLacc
Lac+
--+
+
-+
--+
Lac+
}
Lac-
}
lacI-- dominant
lacOc+ Z+-- Y--+
lacO Z Y
+
-+
lacI+ dominant
in cis and trans
lacOc+ Z+-- Y--+
lacO Z Y
+
+
+
--
Lacc/Lac+
+
Lacc
lacIS Z+ Y+
lacOc Z+ Y+
lacI+c Z--+ Y--+
lacI Z Y
lacI+c Z+-- Y--+
lacI Z Y
lacI--+ Z++ Y++
lacI Z Y
lacI+-- lacO+c
lacI lacO
Z++
Z
Y++
Y
+
+
+
Lacc
}
}
lacOc dominant
in cis
lacOc dominant
in cis even in
presence
of lacI-- 12
genotype
phenotype for: Data of Jacob and Monod, 1961
B-gal
Permease
+IPTG
--IPTG
+IPTG
--IPTG
lacI+ Z+ Y+
+
--
+
--
Lac+
lacIc Z+ Y+
+
-+
+
+
-+
--
+
-+
+
+
-+
--
Lacc
LacLacc
Lac+
--+
+
-+
--+
Lac+
}
Lac-
}
lacI-- dominant
lacOc+ Z+-- Y--+
lacO Z Y
+
-+
lacI+ dominant
in cis and trans
lacOc+ Z+-- Y--+
lacO Z Y
+
+
+
--
Lacc/Lac+
+
Lacc
lacIS Z+ Y+
lacOc Z+ Y+
lacI+c Z--+ Y--+
lacI Z Y
lacI+c Z+-- Y--+
lacI Z Y
lacI--+ Z++ Y++
lacI Z Y
lacI+-- lacO+c
lacI lacO
Z++
Z
Y++
Y
+
+
+
Lacc
}
}
lacOc dominant
in cis
lacOc dominant
in cis even in
presence
of lacI-- 13
genotype
phenotype for: Data of Jacob and Monod, 1961
B-gal
Permease
+IPTG
--IPTG
+IPTG
--IPTG
lacI+ Z+ Y+
+
--
+
--
Lac+
lacIc Z+ Y+
+
-+
+
+
-+
--
+
-+
+
+
-+
--
Lacc
LacLacc
Lac+
--+
+
-+
--+
Lac+
}
Lac-
}
lacIS dominant
lacOc+ Z+-- Y--+
lacO Z Y
+
-+
lacI+ dominant
in cis and trans
lacOc+ Z+-- Y--+
lacO Z Y
+
+
+
--
Lacc/Lac+
+
Lacc
lacIS Z+ Y+
lacOc Z+ Y+
lacI+c Z--+ Y--+
lacI Z Y
lacI+c Z+-- Y--+
lacI Z Y
lacIS+ Z++ Y++
lacI Z Y
lacI+-- lacO+c
lacI lacO
Z++
Z
Y++
Y
+
+
+
Lacc
}
}
lacOc dominant
in cis
lacOc dominant
in cis even in
presence
of lacI-- 14
genotype
phenotype for: Data of Jacob and Monod, 1961
B-gal
Permease
+IPTG
--IPTG
+IPTG
--IPTG
lacI+ Z+ Y+
+
--
+
--
Lac+
lacIc Z+ Y+
+
-+
+
+
-+
--
+
-+
+
+
-+
--
Lacc
LacLacc
Lac+
--+
+
-+
--+
Lac+
}
Lac-
}
lacIS dominant
lacOc+ Z+-- Y--+
lacO Z Y
+
-+
lacI+ dominant
in cis and trans
lacOc+ Z+-- Y--+
lacO Z Y
+
+
+
--
Lacc/Lac+
+
Lacc
lacIS Z+ Y+
lacOc Z+ Y+
lacI+c Z--+ Y--+
lacI Z Y
lacI+c Z+-- Y--+
lacI Z Y
lacIS+ Z++ Y++
lacI Z Y
lacI+-- lacO+c
lacI lacO
Z++
Z
Y++
Y
+
+
+
Lacc
}
}
lacOc dominant
in cis
lacOc dominant
in cis even in
presence
of lacI-- 15
genotype
phenotype for: Data of Jacob and Monod, 1961
B-gal
Permease
+IPTG
--IPTG
+IPTG
--IPTG
lacI+ Z+ Y+
+
--
+
--
Lac+
lacIc Z+ Y+
+
-+
+
+
-+
--
+
-+
+
+
-+
--
Lacc
LacLacc
Lac+
--+
+
-+
--+
Lac+
}
Lac-
}
lacIS dominant
lacOc+ Z+-- Y--+
lacO Z Y
+
-+
lacI+ dominant
in cis and trans
lacOc+ Z+-- Y--+
lacO Z Y
+
+
+
--
Lacc/Lac+
+
Lacc
lacIS Z+ Y+
lacOc Z+ Y+
lacI+c Z--+ Y--+
lacI Z Y
lacI+c Z+-- Y--+
lacI Z Y
lacIS+ Z++ Y++
lacI Z Y
lacI+S
lacI
lacO+c
lacO
Z++
Z
Y++
Y
+
+
+
Lacc
}
}
lacOc dominant
in cis
lacOc dominant
in cis even in
presence
of lacIS 16
17
18
19
20
21
22
Fig. 16.7
23
From: http://www.aw.com/mathews/ch26/c26lara.htm
24
25
26
Attenuation of trp operon
transcription
27
Fig. 16.8
28
29
30
31
32
33
34
Fig. 16.16
35
36
37
38
39
Control of Gene Expression
• Controlling gene expression is often
accomplished by controlling transcription
initiation.
• Regulatory proteins bind to DNA to either
block or stimulate transcription, depending
on how they interact with RNA
polymerase.
40
Control of Gene Expression
• Prokaryotic organisms regulate gene
expression in response to their
environment.
• Eukaryotic cells regulate gene expression
to maintain homeostasis in the organism.
41
Regulatory Proteins
• Gene expression is often controlled by
regulatory proteins binding to specific DNA
sequences.
– regulatory proteins gain access to the
bases of DNA at the major groove
– regulatory proteins possess DNAbinding motifs
42
Regulatory Proteins
• DNA-binding motifs are regions of
regulatory proteins which bind to DNA
– helix-turn-helix motif
– homeodomain motif
– zinc finger motif
– leucine zipper motif
43
Prokaryotic Regulation
• Control of transcription initiation can be:
– positive control – increases
transcription when activators bind DNA
– negative control – reduces
transcription when repressors bind to
DNA regulatory regions called
operators
44
Prokaryotic Regulation
• Prokaryotic cells often respond to their
environment by changes in gene
expression.
• Genes involved in the same metabolic
pathway are organized in operons.
• Some operons are induced when the
metabolic pathway is needed.
• Some operons are repressed when the
metabolic pathway is no longer needed.
45
Prokaryotic Regulation
• The lac operon contains genes for the
use of lactose as an energy source.
• Regulatory regions of the operon include
the CAP binding site, promoter, and the
operator.
• The coding region contains genes for 3
enzymes:
 b-galactosidase, permease, and
transacetylase
46
Prokaryotic Regulation
• The lac operon is negatively regulated by
a repressor protein:
– lac repressor binds to the operator to
block transcription
– in the presence of lactose, an inducer
molecule binds to the repressor protein
– repressor can no longer bind to operator
– transcription proceeds
47
Prokaryotic Regulation
• In the presence of both glucose and lactose,
bacterial cells prefer to use glucose.
• Glucose prevents induction of the lac operon.
– binding of CAP – cAMP complex to the
CAP binding site is required for induction
of the lac operon
– high glucose levels cause low cAMP levels
– high glucose  low cAMP  no induction
48
Prokaryotic Regulation
• The trp operon encodes genes for the
biosynthesis of tryptophan.
• The operon is not expressed when the cell
contains sufficient amounts of tryptophan.
• The operon is expressed when levels of
tryptophan are low.
49
Prokaryotic Regulation
• The trp operon is negatively regulated by
the trp repressor protein
– trp repressor binds to the operator to
block transcription
– binding of repressor to the operator
requires a corepressor which is
tryptophan
– low levels of tryptophan prevent the
repressor from binding to the operator
50
Eukaryotic Regulation
• Controlling the expression of eukaryotic
genes requires transcription factors.
– general transcription factors are
required for transcription initiation
• required for proper binding of RNA
polymerase to the DNA
– specific transcription factors increase
transcription in certain cells or in
response to signals
51
Eukaryotic Transcription
• General transcription factors bind to the
promoter region of the gene.
• RNA polymerase II then binds to the
promoter to begin transcription at the start
site (+1).
• Enhancers are DNA sequences to which
specific transcription factors (activators)
bind to increase the rate of transcription.
52
Eukaryotic Transcription
• Coactivators and mediators are also
required for the function of transcription
factors.
– coactivators and mediators bind to
transcription factors and bind to other
parts of the transcription apparatus
53
Eukaryotic Chromosome Structure
• Eukaryotic DNA is packaged into
chromatin.
• Chromatin structure is directly related to
the control of gene expression.
• Chromatin structure begins with the
organization of the DNA into nucleosomes.
• Nucleosomes may block RNA polymerase
II from gaining access to promoters.
54
Eukaryotic Chromosome Structure
• Methylation (the addition of –CH3) of DNA
or histone proteins is associated with the
control of gene expression.
• Clusters of methylated cytosine nucleotides
bind to a protein that prevents activators
from binding to DNA.
• Methylated histone proteins are associated
with inactive regions of chromatin.
55
Posttranscriptional Regulation
• Control of gene expression usually involves
the control of transcription initiation.
• But gene expression can be controlled after
transcription, with mechanisms such as:
– RNA interference
– alternative splicing
– RNA editing
– mRNA degradation
56
Posttranscriptional Regulation
• RNA interference involves the use of
small RNA molecules
• The enzyme Dicer chops double stranded
RNA into small pieces of RNA
– micro-RNAs bind to complementary
RNA to prevent translation
– small interfering RNAs degrade
particular mRNAs before translation
57
Posttranscriptional Regulation
• Introns are spliced out of pre-mRNAs to
produce the mature mRNA that is translated.
• Alternative splicing recognizes different
splice sites in different tissue types.
• The mature mRNAs in each tissue possess
different exons, resulting in different
polypeptide products from the same gene.
58
Posttranscriptional Regulation
• RNA editing creates mature mRNA that
are not truly encoded by the genome.
• For example –
– apolipoprotein B exists in 2 isoforms
– one isoform is produced by editing the
mRNA to create a stop codon
– this RNA editing is tissue-specific
59
Posttranscriptional Regulation
• Mature mRNA molecules have various
half-lives depending on the gene and the
location (tissue) of expression.
• The amount of polypeptide produced from
a particular gene can be influenced by the
half-life of the mRNA molecules.
60
Protein Degradation
• Proteins are produced and degraded
continually in the cell.
• Proteins to be degraded are tagged with
ubiquitin.
• Degradation of proteins marked with
ubiquitin occurs at the proteasome.
61