Download Regulation of Gene Expression

11
Regulation of Gene
Expression
Chapter 11 Regulation of Gene Expression
Key Concepts
11.1 Many Prokaryotic Genes Are Regulated
in Operons
11.2 Eukaryotic Genes Are Regulated by
Transcription Factors
11.3 Gene Expression Can Be Regulated via
Epigenetic Changes to Chromatin
11.4 Eukaryotic Gene Expression Can Be
Regulated after Transcription
Chapter 11 Opening Question
How does CREB regulate the expression
of many genes?
Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons
Gene expression can be precisely regulated
at many different points:
•  Before or during transcription
•  Before or during translation
•  After translation
Figure 11.1 Potential Points for the Regulation of Gene Expression
Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons
Gene expression begins at the promoter.
Regulatory proteins called transcription
factors control gene activity:
•  Repressors prevent transcription
(negative regulation)
•  Activators stimulate transcription
(positive regulation)
Figure 11.2 Positive and Negative Regulation
Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons
Prokaryotes conserve energy and resources
by making certain proteins only when they
are needed.
They can rapidly change expression levels as
environmental conditions change.
•  Example: lactose catabolism in E. coli
Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons
Uptake and metabolism of lactose involves three
proteins:
•  β-galactoside permease—moves lactose
into the cell
•  β-galactosidase—hydrolyses lactose
•  β-galactoside transacetylase—transfers
acetyl groups to β-galactosides; role is
unclear
If E. coli is grown with glucose but no lactose,
these enzymes are very low (basal level).
Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons
If cells are transferred to lactose medium, they
begin making all 3 enzymes within 10
minutes.
Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons
After lactose is added, the mRNA level
increases before β-galactosidase begins to
rise:
Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons
If lactose is removed, the mRNA level goes
down.
Response of the bacteria to lactose is at the
level of transcription.
Compounds that stimulate transcription of
specific genes are called inducers, the
genes are inducible genes.
Genes that are expressed most the time at a
constant rate are called constitutive genes.
Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons
The three genes for lactose enzymes form an
operon: they are adjacent on the
chromosome, share a promoter, and are
transcribed together.
The lac operon is very efficient but activity can
be reduced when it is not needed—an
example of transcriptional regulation.
Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons
The operon includes an operator—a short
stretch of DNA near the promoter that
controls transcription.
Repressor proteins bind at the operator.
•  Inducible operons are turned off unless
needed.
•  Repressible operons are turned on unless
not needed.
Figure 11.3 The lac Operon of E. coli
Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons
The lac operon is inducible: the repressor
prevents transcription until a β-galactoside
predominates.
A repressor protein is normally bound to the
operator, blocking transcription.
In the presence of lactose, the repressor
detaches and allows RNA polymerase to
initiate transcription.
Figure 11.4 The lac Operon: An Inducible System (Part 1)
Figure 11.4 The lac Operon: An Inducible System (Part 2)
Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons
The repressor protein gene is constitutive
(one that is always active), so the repressor
is always present.
It binds to the operator, but also has an
allosteric binding site for the inducer
(allolactose).
When the inducer binds, the repressor
changes shape and can no longer bind to
the operator.
Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons
The lac repressor gene (lac i) is upstream of
the lac operon.
•  It is a regulatory gene—it encodes a
regulatory protein (transcription factor).
Structural genes encode proteins that are
not directly involved in gene regulation.
Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons
A repressible operon is switched off when its
repressor is bound to its operator.
The repressor only binds in the presence of a
corepressor.
The corepressor causes the repressor to
change shape and bind to the operator to
inhibit transcription.
Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons
The trp operon for tryptophan synthesis is
repressible.
When tryptophan is present in adequate
quantities, the cell can stop making enzymes
for its synthesis.
Tryptophan itself functions is the corepressor:
it binds to the repressor, causing the
repressor to bind to the trp operator to
prevent transcription.
Figure 11.5 The trp Operon: A Repressible System (Part 1)
Figure 11.5 The trp Operon: A Repressible System (Part 2)
Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons
Inducible system—a metabolic substrate
(inducer) interacts with a regulatory protein
(repressor); the repressor cannot bind and
transcription proceeds.
•  Generally controls catabolic pathways.
Repressible system—a metabolic product (corepressor) binds to a regulatory protein,
which then binds to the operator and blocks
transcription.
•  Generally controls anabolic pathways.
Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons
Transcription in prokaryotes can also be
regulated by activator proteins that bind to
DNA sequences at or near the promoter and
promote transcription.
Activators can regulate both inducible and
repressible systems.
Many genes and operons are controlled by
more than one regulatory mechanism.
Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons
Two systems for regulating metabolic
pathways:
•  Allosteric regulation of enzyme activity
(feedback inhibition)
•  Regulation of transcription—slower, but
results in greater savings of energy and
resources
Figure 11.6 Systems to Regulate a Metabolic Pathway
Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons
Sigma factors can bind to RNA polymerase
and direct it to specific promoters.
Global gene regulation: genes that encode
proteins with related functions may be at
different locations but have the same
promoter sequence—thus they can be
expressed at the same time.
•  RNA polymerase is directed to the
promoter in each case by a specific sigma
factor.
Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons
A virus injects its genetic material into a host
cell, often turning it into a virus factory:
Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons
Viruses are not cells and are dependent on
living cells to reproduce.
Viral genomes may be double- or singlestranded DNA or RNA.
Lytic life cycle: the host cell immediately
starts producing new viral particles (virions),
which are released as the cell breaks open,
or lyses
Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons
Lysogenic life cycle: viral genome is
incorporated into host cell genome and is
replicated along with host genome
The virus may survive in this way for many
host cell generations.
An environmental signal can cause the host
cell to start producing virions, and the viral
reproductive cycle enters the lytic phase.
Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons
The lytic cycle has two stages:
•  Early—viral genes adjacent to a promoter
that binds host RNA polymerase are
transcribed.
§ 
Early genes encode proteins that shut
down expression of host genes,
stimulate viral genome replication, and
activate transcription of viral late genes.
•  Late—viral late genes encode viral capsid
proteins and enzymes that lyse the host
cell.
Figure 11.7 A Gene Regulation Strategy for Viral Reproduction
Concept 11.2 Eukaryotic Genes Are Regulated by Transcription
Factors
Eukaryotic cells must also regulate expression
of their genes. Some are constitutive; others
are inducible.
This is especially important in multicellular
organisms.
There are significant differences between
prokaryotes and eukaryotes, which generally
reflect the greater complexity of eukaryotes.
Table 11.1
Concept 11.2 Eukaryotic Genes Are Regulated by Transcription
Factors and DNA Changes
Eukaryotic promoters are DNA regions where
RNA polymerase binds and initiates
transcription.
A common core sequence is the TATA box
(rich in A–T base pairs).
General transcription factors bind to the
core promoter, then RNA polymerase II
binds and initiates transcription.
Figure 11.8 The Initiation of Transcription in Eukaryotes
Concept 11.2 Eukaryotic Genes Are Regulated by Transcription
Factors
Other promoter sequences are specific to a
few genes and are recognized by specific
transcription factors.
Concept 11.2 Eukaryotic Genes Are Regulated by Transcription
Factors
DNA sequences that bind activators are
enhancers, those that bind repressors are
silencers.
The combination of factors present
determines whether transcription is initiated.
Concept 11.2 Eukaryotic Genes Are Regulated by Transcription
Factors
Transcription factors recognize particular
nucleotide sequences.
•  Example: NFATs (nuclear factors of
activated T cells) control genes in the
immune system.
NFAT proteins bind to a recognition sequence
by hydrogen bonding and hydrophobic
interactions.
There is an induced fit between the NFAT and
the DNA, and the protein undergoes a
conformational change.
Figure 11.9 A Transcription Factor Protein Binds to DNA
Concept 11.2 Eukaryotic Genes Are Regulated by Transcription
Factors
In multicellular organisms, all differentiated
cells contain the entire genome; their specific
characteristics arise from differential gene
expression.
Figuring out how to get undifferentiated cells,
such as fibroblasts, to differentiate into
specialized cells, such as neurons, may
prove to be effective in treating many
diseases, such as Alzheimer’s, which
involves degeneration of neurons.
Figure 11.10 Expression of Specific Transcription Factors Turns Fibroblasts into Neurons (Part 1)
Figure 11.10 Expression of Specific Transcription Factors Turns Fibroblasts into Neurons (Part 2)
Figure 11.10 Expression of Specific Transcription Factors Turns Fibroblasts into Neurons (Part 3)
Concept 11.2 Eukaryotic Genes Are Regulated by Transcription
Factors
Coordination of gene expression:
Even if they are far apart, genes can share
regulatory sequences that bind the same
transcription factors.
•  Example: plant response to drought—the
scattered stress response genes all have
a regulatory sequence called the
dehydration response element.
§  The resulting proteins help the plant
conserve water and protect against
freezing or excess salt.
Figure 11.11 Coordinating Gene Expression
Concept 11.2 Eukaryotic Genes Are Regulated by Transcription
Factors
Human immunodeficiency virus (HIV) has a
complex life cycle.
It infects only cells in the immune system that
have the surface receptor CD4.
The virion is enclosed in a membrane from the
previous host cell, which fuses with the new
host cell’s membrane.
Figure 11.12 The Reproductive Cycle of HIV
Concept 11.2 Eukaryotic Genes Are Regulated by Transcription
Factors
HIV is a retrovirus: its genome is singlestranded RNA.
After infection, reverse transcriptase makes
a DNA strand that is complementary to the
RNA, while at the same time degrading the
RNA and making a second DNA strand.
The resulting double-stranded DNA is
integrated into the host’s chromosome.
The integrated viral DNA is called a provirus.
Concept 11.2 Eukaryotic Genes Are Regulated by Transcription
Factors
The provirus resides permanently in the host
chromosome and can be inactive for years.
Transcription of the viral DNA may be
initiated, but host cell proteins (termination
factors) prevent the RNA from elongating.
Figure 11.13 Regulation of Transcription by HIV
Concept 11.2 Eukaryotic Genes Are Regulated by Transcription
Factors
Under some circumstances, a viral gene
encodes Tat (Transactivator of transcription),
which allows RNA polymerase to transcribe
the viral genome.
The rest of the viral reproductive cycle is then
able to proceed.
After discovery of this mechanism,
researchers found that many eukaryotic
genes are regulated at the level of
transcription elongation.
Concept 11.3 Gene Expression Can Be Regulated via Epigenetic
Changes to Chromatin
Gene transcription can also be regulated by
reversible alterations to DNA or
chromosomal proteins—epigenetic
changes.
Although base sequences are not changed,
these alterations can be passed on to
daughter cells.
One type of alteration is chromatin
remodeling.
Concept 11.3 Gene Expression Can Be Regulated via Epigenetic
Changes to Chromatin
DNA is packaged into nucleosomes—
positively charged histone proteins around
which DNA is wound:
Concept 11.3 Gene Expression Can Be Regulated via Epigenetic
Changes to Chromatin
The “tails” have positively charged amino
acids, especially lysine.
There is strong ionic attraction between the
positive histone proteins and DNA
(negatively charged because of phosphate
groups).
Thus, nucleosomes can make DNA physically
inaccessible to RNA polymerase.
Concept 11.3 Gene Expression Can Be Regulated via Epigenetic
Changes to Chromatin
Histone acetyltransferases can add acetyl
groups to the positive amino acids and
neutralize them:
Concept 11.3 Gene Expression Can Be Regulated via Epigenetic
Changes to Chromatin
Reducing positive charges on the histone tails
reduces affinity of the histones for the DNA,
loosening the compact nucleosome.
Histone acetylation promotes both
transcription initiation and elongation.
Histone acetylases can be recruited to
promoters by transcription factors, such as
CREB.
Figure 11.14 Epigenetic Remodeling of Chromatin for Transcription
Concept 11.3 Gene Expression Can Be Regulated via Epigenetic
Changes to Chromatin
Histone deacetylase removes acetyl groups
from histones, repressing transcription.
Histones can also be modified by methylation
(addition of methyl groups) and
phosphorylation (addition of a phosphate
groups).
All these effects are reversible, so
transcriptional activity may be determined by
varying patterns of histone modification.
Concept 11.3 Gene Expression Can Be Regulated via Epigenetic
Changes to Chromatin
Cytosines in DNA are chemically modified by
addition of a methyl group (—CH3) to form 5methylcytosine, catalyzed by DNA
methyltransferase.
In mammals this usually occurs on cytosines
(C) that are adjacent to guanines (G).
CpG sites are nearly always methylated.
Promoters have regions rich in C and G,
called CpG islands.
Figure 11.15 DNA Methylation: An Epigenetic Change (Part 1)
Figure 11.15 DNA Methylation: An Epigenetic Change (Part 2)
Concept 11.3 Gene Expression Can Be Regulated via Epigenetic
Changes to Chromatin
Methylated DNA binds proteins involved in
repression of transcription; heavily
methylated genes tend to be inactive
(silenced).
DNA methylation is usually a stable, long-term
silencing mechanism.
When DNA replicates, maintenance
methyltransferase catalyzes formation of 5methylcytosine in the new DNA strand.
Concept 11.3 Gene Expression Can Be Regulated via Epigenetic
Changes to Chromatin
But methylation is reversible, so methylation
patterns can be altered.
Demethylase catalyzes removal of methyl
groups from cytosine.
Genes whose products are needed are kept
unmethylated, and their associated histones
acetylated.
Concept 11.3 Gene Expression Can Be Regulated via Epigenetic
Changes to Chromatin
Two kinds of chromatin are visible during
interphase:
•  Euchromatin—diffuse and light-staining;
unmethylated; DNA is available for
transcription
•  Heterochromatin—condensed, darkstaining, methylated; contains genes not
transcribed
Concept 11.3 Gene Expression Can Be Regulated via Epigenetic
Changes to Chromatin
A type of heterochromatin is the inactive X
chromosome in mammals.
Early in the development of a female, one of
the X chromosomes becomes
heterochromatic and transcriptionally
inactive.
Which X becomes inactive is random; in one
embryonic cell the paternal X might be
inactivated, but in a neighboring cell the
maternal X might be inactivated.
Concept 11.3 Gene Expression Can Be Regulated via Epigenetic
Changes to Chromatin
Example of a
phenotype caused
by X chromosome
inactivation: the
tortoiseshell cat.
Concept 11.3 Gene Expression Can Be Regulated via Epigenetic
Changes to Chromatin
The inactive X is identifiable in the nucleus as
a heterochromatic Barr body.
Concept 11.3 Gene Expression Can Be Regulated via Epigenetic
Changes to Chromatin
Methylation patterns are stable and can be
passed from one generation to the next.
But studies of monozygotic twins show they
can be altered.
Comparison of DNA in such twin pairs shows
that in 3-year-olds, DNA methylation patterns
are virtually the same.
By age 50, when twins have been living in
different environments—the patterns are
different, and different genes are expressed.
Concept 11.3 Gene Expression Can Be Regulated via Epigenetic
Changes to Chromatin
These studies show that environment plays an
important role in epigenetic modifications,
and thus gene regulation.
Environmental factors that may be involved
include chemicals in tobacco smoke, dietary
components, and stress.
Concept 11.3 Gene Expression Can Be Regulated via Epigenetic
Changes to Chromatin
Genomic imprinting:
In mammals, DNA methylation patterns in
sperm differs from that in eggs at about 200
genes.
A given gene in this group may be methylated
in eggs but unmethylated in sperm. The
offspring would inherit one methylated copy
and one unmethylated copy.
Most imprinted genes are involved with
embryonic development.
Concept 11.4 Eukaryotic Gene Expression Can Be Regulated
after Transcription
Eukaryotic gene expression can be regulated
after transcription.
Different mRNAs can be made from one gene
by alternative splicing: different
combinations of introns are spliced together.
Figure 11.16 Alternative Splicing Results in Different Mature mRNAs and Proteins
Concept 11.4 Eukaryotic Gene Expression Can Be Regulated
after Transcription
Examples of alternative splicing:
•  The HIV genome encodes nine proteins,
but is transcribed as a single pre-mRNA.
•  In Drosophila, sex is determined by the
Sxl gene, which has four exons.
Splicing generates different exon combinations
in males and females.
Concept 11.4 Eukaryotic Gene Expression Can Be Regulated
after Transcription
Some noncoding regions of DNA are
transcribed into microRNA (miRNA).
miRNA was discovered in C. elegans during
research on genes that control larval
development stages:
•  lin-14 encodes a transcription factor for
genes that control events in the 1st stage.
•  lin-4 negatively regulates lin-14, so cells
can progress to the next stage. It encodes
an miRNA that inhibits lin-14 expression
by binding to its mRNA.
Concept 11.4 Eukaryotic Gene Expression Can Be Regulated
after Transcription
Many miRNAs have now been described.
Once transcribed, they are folded and
processed, then guided to a target mRNA by
protein complexes.
Translation is thus inhibited and the mRNA is
degraded.
This mechanism is found in most eukaryotes,
indicating its importance and that it is
evolutionarily ancient.
Figure 11.17 mRNA Degradation Caused by MicroRNAs
Concept 11.4 Eukaryotic Gene Expression Can Be Regulated
after Transcription
Amounts of proteins and their mRNAs in a cell
are not consistently related.
Protein concentrations can be adjusted by
regulating mRNA translation or altering how
long proteins persist.
Concept 11.4 Eukaryotic Gene Expression Can Be Regulated
after Transcription
Three ways to regulate mRNA translation:
•  Inhibit translation with miRNAs
•  Modify the 5′ cap of mRNA. If the cap is
unmodified mRNA is not translated.
•  Translational repressor proteins bind to
mRNAs and prevent their attachment to
ribosomes.
§ 
Example: ferritin binds free Fe2+ ions;
when it is low, a repressor binds to the
ferritin mRNA.
Figure 11.18 A Repressor of Translation
Concept 11.4 Eukaryotic Gene Expression Can Be Regulated
after Transcription
Protein content of any cell at a given time is a
function of synthesis and degradation.
Proteins can be targeted for destruction when
an enzyme attaches a ubiquitin to a lysine.
Other ubiquitins then attach to form a protein–
polyubiquitin complex.
The complex binds to a proteasome where the
polyubiquitin is removed and the protein is
digested by proteases.
Figure 11.19 A Proteasome Breaks Down Proteins
Answer to Opening Question
The CREB family of transcription factors can
activate or repress gene expression by
binding to the cAMP response element
(CRE) sequence found in the promoter
region of many genes.
CREB binding is essential in many organs,
including the brain, and plays a role in drug
and alcohol addiction.
Figure 11.20 An Explanation for Alcoholism?
Answer to Opening Question
CREB also has a role in long-term memory.
When animals learn a task, imaging studies
show CRE-containing genes becoming
active in the hippocampus.
CREB provides insights into the molecular
biology of memory, linking learning to the
regulation of gene expression.