Chapter 18:
Regulation of Gene Expression
AP Biology
Overview: Conducting the Genetic Orchestra
•
Prokaryotes and eukaryotes alter gene expression in response to changes in
environmental conditions
–
Multicellular eukaryotes must also develop and maintain multiple cell types
•
Though multicellular eukaryotes have different types of cells, all of these
cells contain the same genome
–
A significant challenge in the gene regulation of these organisms is
controlling the expression of different subsets of genes to create
different cell types
•
Gene expression is often regulated at the stage of transcription, but control at other
levels of gene expression is also important
–
RNA molecules play many roles in regulating gene expression in eukaryotes
Concept 18.1:
Bacteria often respond to
environmental change by regulating
transcription
Regulation of Enzyme Activity and Production
•
Natural selection has favored bacteria that produce only the products needed by that
cell
–
•
By doing so, these bacteria can conserve resources and energy for other
important tasks
Metabolic control occurs on 2 levels:
–
First, cells can adjust the activity of enzymes that are already present by
feedback inhibition
Precursor
Fig. 18-2
•
–
In this type of inhibition, the
activity of an enzyme is inhibited
by a product in an anabolic
pathway
Second, cells can adjust the
production level of certain enzymes
by regulating the expression of the
genes encoding these enzymes
Feedback
inhibition
trpE gene
Enzyme 1
trpD gene
Regulation
of gene
expression
Enzyme 2
trpC gene
trpB gene
Enzyme 3
trpA gene
•
Gene expression in bacteria is
controlled by the operon model
Tryptophan
(a) Regulation of enzyme
activity
(b) Regulation of enzyme
production
Operons: The Basic Concept
• A cluster of functionally related genes can be under
coordinated control by a single on-off “switch”
– The regulatory “switch” is a segment of DNA called an
operator usually positioned within the promoter
• The operator controls access of RNA polymerase to the
genes
• An operon is the entire stretch of DNA that includes the
operator, the promoter, and the genes that they control
Repressors
• The operon can be switched off by a protein repressor
–
The repressor prevents gene transcription by binding to the
operator and blocking RNA polymerase (no transcription)
–
A repressor protein is specific for the operator of a particular
operon
–
The repressor is the product of a separate regulatory gene
• Regulatory genes are expressed continuously, although at a
low rate, so that a few repressor molecules are always
present within the cell
Repressors (Continued)
•
The binding of repressors to operators is reversible
•
Operators can be in one of 2 states at any given time:
•
One with repressor bound (“off” mode)
•
One without the repressor bound (“on” mode)
•
•
The relative duration of each state depends on the number of active
repressor molecules present
The repressor can be in an active or inactive form, depending on the presence
of other molecules
•
In its inactive form, the repressor has little affinity for its operator
•
In its active form, a specific substrate binds to the repressor at an allosteric
site, triggering a change in conformation
•
These types of substrates are examples of molecules called
corepressors that cooperates with a repressor protein to switch an
operon off
•
Ex) E. coli can synthesize the amino acid tryptophan
Operon “On”
• By default the trp operon is on and the genes for tryptophan
synthesis are transcribed
Fig. 18-3a
•
Occurs when tryptophan is absent
•
Repressor is inactive
trp operon
Promoter
Promoter
Genes of operon
DNA
trpR
Regulatory
gene
mRNA
5
Protein
trpE
3
Operator
Start codon
mRNA 5
RNA
polymerase
Inactive
repressor
trpD
trpC
trpB
trpA
B
A
Stop codon
E
D
C
Polypeptide subunits that make up
enzymes for tryptophan synthesis
(a) Tryptophan absent, repressor inactive, operon on
Operon “Off”
• When tryptophan is present, it binds to the trp repressor protein,
which turns the operon off
•
The repressor is active only in the presence of its corepressor
tryptophan
Fig. 18-3b-2
•
Thus the trp operon is turned off (repressed) if tryptophan levels
are high
DNA
No RNA made
mRNA
Protein
Active
repressor
Tryptophan
(corepressor)
(b) Tryptophan present, repressor active, operon off
Repressible and Inducible Operons:
Two Types of Negative Gene Regulation
•
There are 2 types of negative gene regulation:
–
1) A repressible operon is one that is usually on
• Binding of a repressor to the operator shuts off transcription
– Ex) trp operon
–
2) An inducible operon is one that is usually off
•
A molecule called an inducer inactivates the repressor and turns
on transcription
– Ex) lac operon
The lac Operon: An Inducible Operon
•
The lac operon is an inducible operon found in E.coli cells
–
This operon contains genes that code for enzymes used in the hydrolysis and
metabolism of lactose
•
Lactose metabolism begins with the hydrolysis of lactose into its
component monosaccharides – glucose and galactose
– This reaction is catalyzed by the enzyme β- galactosidase
–
The gene for β-galactosidase is one of the 3 genes that code for
enzymes that function in lactose utilization
•
The entire transcription unit is under the command of a single operator and
promoter
•
A regulatory gene located outside the operon called lacI codes for an
allosteric repressor protein that can switch the operon “off” by binding to
the operator
The lac Operon: Allolactose as an Inducer
•
A molecule called an inducer inactivates the repressor to turn the lac operon on
–
For the lac operon, the inducer is an isomer of lactose called allolactose
•
–
Allolactose is formed in small amounts from lactose that enters the cell
Allolactose binds to the lac repressor and alters its shape, preventing the
repressor from binding to the operator
Fig. 18-4b
•
Without a bound repressor, the lac operon is transcribed into mRNA, and
the proteins needed for lactose utilization are produced
lac operon
DNA
lacZ
lacY
-Galactosidase
Permease
lacI
3
mRNA
5
RNA
polymerase
mRNA 5
Protein
Allolactose
(inducer)
lacA
Inactive
repressor
(b) Lactose present, repressor inactive, operon on
Transacetylase
The lac Operon: Lactose Absent
• By itself, the lac repressor is active and switches the lac operon off
–
Occurs due to the absence of lactose (and hence allolactose)
Fig. 18-4a
Regulatory
gene
Promoter
Operator
lacI
DNA
lacZ
No
RNA
made
3
mRNA
5
Protein
RNA
polymerase
Active
repressor
(a) Lactose absent, repressor active, operon off
Inducible vs. Repressible Enzymes
•
The enzymes of the lactose pathway are referred to as inducible enzymes because
their synthesis is induced by a chemical signal (allolactose)
–
•
Inducible enzymes usually function in catabolic pathways
The enzymes for tryptophan synthesis are referred to as repressible enzymes
because their synthesis is repressed by high levels of the end product
–
•
Repressible enzymes usually function in anabolic pathways
Regulation of both the trp and lac operons involves negative control of genes
because operons are switched off by the active form of the repressor
–
Gene regulation is said to be positive only when a regulatory protein interacts
directly with the genome to switch transcription on
Positive Gene Regulation
•
An example of positive gene regulation also involves the lac operon
–
When glucose and lactose are both present, E.coli preferentially use glucose,
since the enzymes for glycolysis are always present
•
–
E.coli use lactose as an energy source only when glucose is in short
supply
When glucose is scarce, a small organic molecule called cyclic AMP (cAMP)
accumulates
•
In this case, the lac operon is subject to positive control through a
stimulatory protein called catabolite activator protein (CAP), an activator
of transcription
•
CAP is activated by binding
with cAMP, which allows it to
attach to a specific site at the
upstream end of the lac promoter
•
This attachment increases the
affinity of RNA polymerase for the
promoter, thus accelerating
transcription
Dual Control of the lac Operon
•
•
When glucose levels in the cell increase, cAMP concentration decreases
–
Without cAMP, CAP detaches from the lac operon
–
Because CAP is inactive, the affinity of RNA polymerase for the promoter of the
lac operon is lowered
–
Transcription of the lac operon will
thus proceed only at a low level, even
in the presence of lactose
Therefore, the lac operon is under dual control:
–
Negative control by the lac repressor
(like on-off switch)
•
–
Positive control by CAP (like volume control)
•
•
The state of the lac repressor (with or without bound allolactose)
determines whether transcription of the lac operon’s genes will occur at all
The state of CAP (with or without bound cAMP) controls the rate of
transcription if the operon is repressor-free
CAP also helps regulate other operons that encode enzymes used in catabolic
pathways
Concept 18.2:
Eukaryotic gene expression can be
regulated at any stage
Gene Expression and Cell Specialization
• All organisms must regulate which genes are expressed at any
given time
– In multicellular organisms gene expression is essential for
cell specialization
• To perform its role, each cell type must maintain a
specific program of gene expression in which certain
genes are expressed and others are not
Differential Gene Expression
•
Almost all the cells in an organism are genetically identical
–
Differences between cell types result from differential gene
expression, the expression of different genes by cells with the same
genome
• A typical human cell expresses only ~20% of its genes at any given
time
–
•
Errors in gene expression can lead to diseases including cancer
Gene expression in eukaryotic cells is regulated at many stages
–
Each stage is a potential control point at which gene expression can be
turned on or off, accelerated, or slowed down
Regulation of Gene Expression at Transcription
• In all organisms, a common control point for gene expression is at
transcription
–
Regulation at this stage is often in response to signals
(hormones, signaling molecules) coming from outside the cell
–
For this reason, the term “gene expression” is often equated with
transcription for both bacteria and eukaryotes
• The greater complexity of eukaryotes, however, also
provides opportunities for regulating gene expression at
many additional stages
Fig. 18-6
•
Signal
In this diagram, the colored boxes indicate
NUCLEUS
Chromatin
processes most often regulated
–
Chromatin modification
DNA
Gene available
for transcription
Each color indicates the type of
Gene
molecule affected (blue=DNA,
Transcription
RNA
Exon
Primary transcript
orange=RNA, purple=protein)
Intron
RNA processing
Tail
–
The nuclear envelope separating
Cap
mRNA in nucleus
Transport to cytoplasm
transcription and translation in
CYTOPLASM
mRNA in cytoplasm
eukaryotic cells offers opportunities
for post-transcriptional control in the
Degradation
of mRNA
Translatio
n
Polypeptide
form of RNA processing
Protein processing
–
In addition, eukaryotes have a greater
variety of control mechanisms
operating before transcription and
after translation
Active protein
Degradation
of protein
Transport to cellular
destination
Cellular function
Regulation of Chromatin Structure
• The structural organization of chromatin not only packs a cell’s DNA
into a compact form that fits inside the nucleus, but it also helps
regulate gene expression in several ways
–
The location of a gene’s promoter can affect whether a gene will
be transcribed
–
In addition, genes within highly packed heterochromatin are
usually not expressed
–
Chemical modifications to histones and DNA of chromatin also
influence both chromatin structure and gene expression
Histone Modifications
•
There is mounting evidence that chemical modifications to histones play a
direct role in regulation of gene transcription
–
The N-terminus of each histone molecule protrudes outward from the
nucleosome
–
Fig. 18-7
These histone tails are
accessible to various
modifying enzymes that
Histone
tails
catalyze the addition or
removal of specific
chemical groups
DNA
double helix
Amino
acids
available
for chemical
modification
(a) Histone tails protrude outward from a
nucleosome
Histone Acetylation
•
Histone
tails
In histone acetylation, acetyl groups (-COCH3) are attached to positively
charged lysines in histone tails
–
When lysines are acetylated,
DNA
double
helix
their
positive
charges are
Amino
acids
available
for chemical
modification
neutralized
• As a result, histone tails no longer bind to neighboring
nucleosomes
–
(a) Histone tails protrude outward from a
nucleosome
This process loosens chromatin structure and allows transcription
proteins easier access to
genes, thereby promoting
the initiation of
transcription
Unacetylated histones
Acetylated histones
(b) Acetylation of histone tails promotes loose
chromatin structure that permits transcription
Other Histone Modifications
•
Several other chemical groups can be reversibly attached to amino acids in
histone tails, including methyl and phosphate groups
–
The addition of methyl groups (methylation) can condense chromatin
–
The addition of phosphate groups (phosphorylation) next to a methylated
amino acid can loosen chromatin
•
The discovery that these and other modifications to histone tails can affect
chromatin structure and gene expression has led to the histone code hypothesis
–
This hypothesis proposes that specific combinations of modifications,
rather than the overall level of histone acetylation, help determine
chromatin configuration
•
Chromatin configuration, in turn, has a direct influence on transcription
DNA Methylation
•
Some enzymes can methylate certain bases of DNA itself
–
DNA methylation, the addition of methyl groups to certain bases in DNA, is
associated with reduced transcription in some species
•
–
Ex) The inactivated mammalian X chromosome is generally more
methylated than DNA that is actively transcribed
DNA methylation can also cause long-term inactivation of genes in cellular
differentiation
•
Methylation patterns are passed on to successive generations of cells, so
that cells keep a chemical record of what occurred during embryonic
development
•
A methylation pattern maintained in this way accounts for genomic
imprinting in mammals
–
In genomic imprinting, methylation regulates expression of either the
maternal or paternal alleles of certain genes at the start of
development
Epigenetic Inheritance
• Although 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
• Epigenetic variations might help explain why one
identical twin acquires a genetically based disease
(schizophrenia), but the other does not, despite their
identical genomes
Regulation of Transcription Initiation
•
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
–
Once the chromatin of a gene is optimally modified for expression, the
initiation of transcription is the next major step at which gene
expression is regulated
• Involves proteins that bind to DNA and either facilitate or inhibit
binding of RNA polymerase (transcription factors)
• Before looking at how eukaryotic cells control transcription,
however, it is helpful to review the structure of a typical eukaryotic
gene
•
In a typical eukaryotic gene, a cluster of proteins called a transcription initiation
complex assembles on the promoter sequence at the “upstream” end of a gene
–
One of these proteins (RNA polymerase II) then proceeds to transcribe the
gene, producing a primary RNA transcript
•
–
RNA processing follows, including enzymatic addition of a 5’ cap and a
poly-A tail, as well as splicing out of introns
Associated with most eukaryotic genes are control elements, segments of
noncoding
DNA that help regulate transcription by binding certain proteins
Fig. 18-8-3
•
Control elements and the proteins they bind are critical to the precise
regulation of gene expression in different cell types
Enhancer
(distal control elements)
Poly-A signal
sequence
Termination
region
Proximal
control elements
Exon
Intron
Exon
Intron Exon
DNA
Upstream
Downstream
Promoter
Primary RNA
5
transcript
Transcription
Exon
Intron
Exon
Intron Exon
RNA processing
Cleaved 3 end
of primary
transcript
Poly-A
signal
Intron RNA
Coding segment
mRNA
3
5 Cap
5 UTR
Start
codon
Stop
codon
3 UTR Poly-A
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 proteincoding genes
•
Most of these transcription factors do not bind DNA directly, but bind to
proteins (including each other) and RNA polymerase II
•
These protein-protein interactions are crucial to the initiation of eukaryotic
transcription
•
The interactions of general transcription factors and RNA polymerase II
with a promoter, however, usually only lead to a low rate of transcription
–
In eukaryotes, high levels of transcription of particular genes depend on control
elements interacting with another set of proteins called specific transcription
factors
Proximal vs. Distal Control Elements
•
Some of these specific transcription factors are called proximal control
elements because they are located close to the promoter
•
More distant groups of specific transcription factors called enhancers may
be located 1000s of nucleotides upstream or downstream of a gene, or even
within an intron
–
These enhancers are referred to as distal control elements
• A given gene may have multiple enhancers, each active at a
different time or in a different cell type or location within an
organism
• Each enhancer, however, is only associated with one specific gene
Activators and Mediator Proteins
•
In eukaryotes, the rate of gene expression can be strongly controlled by the binding
of special proteins to the control elements of enhancers
–
An activator is a protein that binds to an enhancer and stimulates transcription
of a gene
•
Protein-mediated bending of DNA is thought to bring bound activators in
contact with another group of proteins called mediator proteins
–
These mediator proteins will, in turn, interact with proteins at the
promoter
•
These multiple protein-protein interactions help assemble and position the
initiation complex on the promoter
Animation: Initiation of Transcription
•
Step 1: Activator proteins bind to distal control elements grouped as an enhancer in
the DNA
–
•
Step 2: A DNA-bending protein brings the bound activator closer to the promoter
–
•
This particular enhancer has 3 binding sites
General transcription
factors, mediator
proteins, and RNA
polymerase are
nearby
Step 3: The activator bind
to certain mediator proteins
and general transcription
factors, helping them form
an active transcription
initiation complex on
the promoter
Fig. 18-9-3
Promoter
Activators
DNA
Enhancer
Distal control
element
Gene
TATA
box
General
transcription
factors
DNA-bending
protein
Group of
mediator proteins
RNA
polymerase II
RNA
polymerase II
Transcription
initiation complex
RNA synthesis
•
Some transcription factors function as repressors, inhibiting expression of a
particular gene
–
Some repressors bind directly to control element DNA, like enhancers
•
This may block activator binding or turn off transcription even when
activators are bound
–
Other repressors block the binding of activators to proteins that allow activators
to bind to DNA
•
Some activators and repressors act indirectly by influencing chromatin structure to
promote or silence transcription
–
Activators may recruit proteins that acetylate histones near the promoters of
specific genes, thereby promoting transcription
–
Some repressors recruit proteins that deacetylate histones, leading to reduced
transcription
Coordinately Controlled Genes in Eukaryotes
•
In bacteria, coordinately controlled genes are often clustered in an operon that is
regulated by a single promoter and transcribed in a single mRNA molecule
–
In eukaryotic cells, some co-expressed genes are also clustered near one
another of the same chromosomes, but each has its own promoter and control
elements
–
More commonly, however, these genes are scattered over different
chromosomes, but each has the same combination of control elements
•
Copies of the activators recognize these specific control elements and
promote simultaneous transcription of the genes, no matter where they are
in a genome
–
This coordinated control often occurs in response to chemical signals
(ex: hormones) from outside the cell
•
–
These signals bind to receptor proteins, forming complexes that
serves as transcription activators
Every gene whose transcription is stimulated by a particular chemical
signal has a control element recognized by the same complex,
regardless of its chromosomal location
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
•
RNA processing in the nucleus and export of mature RNA to the cytoplasm provide
several opportunities for regulating gene expression in eukaryotic cells
–
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
•
Regulatory proteins specific to each cell type control intron-exon choices
Fig. 18-11
by binding to regulatory sequences
Exons
in the primary transcript
DNA
–
Troponin T gene
Ex) The troponin T
encodes 2 different
proteins
Primary
RNA
transcript
RNA splicing
mRNA
or
gene
mRNA Degradation
•
The life span of mRNA molecules in the cytoplasm is a key to determining
protein synthesis
–
Eukaryotic mRNA is more long lived than prokaryotic mRNA, allowing
them to be translated repeatedly in these cells
–
The mRNA life span is determined in part by sequences in the leader
and trailer regions
• Nucleotide sequences that affect how long an mRNA remains
intact are often found in the untranslated region (UTR) at the 3’ end
Animation: mRNA Degradation
Initiation of Translation
•
Translation presents another opportunity for regulating gene expression
–
Occurs most commonly at the initiation stage
•
The initiation of translation of some mRNAs can be blocked by regulatory
proteins that bind to sequences or structures within the 5’ UTR of the
mRNA
– This prevents attachment of ribosomes and hence translation
•
Alternatively, translation of all mRNAs
in a cell may be regulated simultaneously
–
Usually involves activation or inactivation of one or more protein
factors required to initiate translation
•
Ex) Translation initiation factors are simultaneously
activated in an egg following fertilization
Animation: Blocking Translation
Protein Processing and Degradation
•
The final opportunity for controlling gene expression occurs after translation
–
Eukaryotic polypeptides must often be processed to yield functional protein
molecules
•
These various types of protein processing include cleavage and chemical
modifications
–
–
Ex) Regulatory proteins are commonly activated or inactivated by the
reversible addition of phosphate groups
The length of time each protein functions in a cell is also strictly regulated by
means of selective degradation
•
To mark a particular protein for destruction, the cell often attaches
molecules of a small protein called ubiquitin to that protein
•
Giant protein complexes called proteasomes recognize these ubiquitintagged proteins and degrade them
Animation: Protein Degradation
Animation: Protein Processing
Degradation of a Protein by a Proteasome
•
Step 1: Multiple ubiquitin molecules are attached to a protein by enzymes in
the cytosol
•
Step 2: The ubiquitin-tagged protein is recognized by a proteasome , which
unfolds the protein and sequesters it within a central cavity
Fig. 18-12
•
Step 3: Enzymatic components of the proteasome cut the protein into small
peptides, which can be further degraded by other enzymes in the cytosol
Ubiquitin
Proteasome
Protein to
be degraded
Ubiquitinated
protein
Proteasome
and ubiquitin
to be recycled
Protein entering a
proteasome
Protein
fragments
(peptides)
Concept 18.3:
Noncoding RNAs play multiple roles
in controlling gene expression
Noncoding RNAs and Regulation of Gene Expression
• Only a small fraction (1.5% in humans) of DNA codes for
proteins, rRNA, and tRNA
– A significant amount of the genome may be transcribed into
noncoding RNAs
• Noncoding RNAs regulate gene expression at two
points:
– mRNA translation
– Chromatin configuration
Effects on mRNAs by MicroRNAs and Small
Interfering RNAs
•
MicroRNAs (miRNAs) are small single-stranded RNA molecules that can bind to
complementary sequences of mRNA
–
miRNAs are formed from longer RNA precursors that fold back on themselves,
forming one or more double-stranded hairpin structures, each held together by
hydrogen bonds
–
After each hairpin is cut away from the precursor, it is trimmed by an enzyme
called a Dicer into a short, double-stranded fragment of ~20 nucleotide pairs
–
One of the two strands is degraded, while the other strand (the miRNA) forms a
complex with one or more proteins
•
The miRNA allows this complex to bind to any mRNA molecule with a
complementary sequence
•
The miRNA-protein complex then either degrades the target mRNA or
blocks its translation
–
The expression of an estimated 1/3 of all human genes may be
regulated by miRNAs
•
Step 1: An enzyme cuts each hairpin from the primary miRNA transcript
•
Step 2: A second enzyme called Dicer trims the loop and the single-stranded ends
from the hairpin (cuts are made at the arrows)
•
Step 3: One strand of the double-stranded RNA is degraded
–
•
The other strand (miRNA) than forms a complex with one or more proteins
Step 4: The miRNA in the complex can bind to any target mRNA that contains at
Fig. 18-13
least 6 bases of complementary
Hairpin
miRNA
Hydrogen
bond
sequence
Dicer
•
Step 5: If miRNA and mRNA
bases are complementary all
along their length, the
miRNA
5 3
(a) Primary miRNA transcript
miRNAprotein
complex
mRNA is degraded (left)
–
If the match is less
complete, translation
is blocked (right)
mRNA degraded
Translation blocked
(b) Generation and function of miRNAs
Small Interfering RNAs
•
Gene expression can also be blocked by RNA molecules called small
interfering RNAs (siRNAs)
–
The phenomenon of inhibition of gene expression by RNA molecules is
called RNA interference (RNAi)
• siRNAs and miRNAs are similar but form from different RNA
precursors
– miRNA is formed from a single hairpin in a precursor RNA
– siRNAs are formed from much longer double-stranded RNA
molecules, each which gives rise to many siRNAs
Chromatin Remodeling and Silencing of
Transcription by Small RNAs
•
Small RNA molecules can also cause remodeling of chromatin structure
–
siRNAs play a role in heterochromatin formation and can block large
regions of the chromosome
• An RNA transcript produced from DNA is copied into doublestranded RNA, which is then processed into several siRNAs
• These siRNAs associate with a complex of proteins, which then
recruit enzymes that modify the chromatin, turning it into the highly
condensed heterochromatin
–
Small RNAs may also block transcription of specific genes
Concept 18.4:
A program of differential gene
expression leads to the different cell
types in a multicellular organism
A program of differential gene expression leads to the
different cell types in a multicellular organism
• During embryonic development, a fertilized egg gives rise to
many different cell types
– Cell types are organized successively into tissues, organs,
organ systems, and the whole organism
• Gene expression orchestrates this developmental
program, producing cells of different types that form
these higher-level structures
A Genetic Program for Embryonic Development
•
The transformation from zygote to adult results from 3 interrelated processes:
–
Cell division
•
The zygote gives rise to a large number of cells through a succession of
mitotic cell division
–
Cell differentiation
•
–
These daughter cells then become specialized in structure and function
Fig. 18-14
Morphogenesis
•
These different types of
cells are organized into
tissues and organs in a
particular 3-dimensional
arrangement that give an
organism its shape
(a) Fertilized eggs of a frog
(b) Newly hatched tadpole
• Differential gene expression results from genes being
regulated differently in each cell type
– Materials placed into an egg by the mother set up
a sequential program of gene regulation that is
carried out as cells divide
– This program makes the cells become different
from each other in a coordinated fashion
Cytoplasmic Determinants and Inductive Signals
•
Two sources of information “tell” a cell which genes to express at any given time
during embryonic development
–
An egg’s cytoplasm contains RNA, proteins, and other substances that are
distributed unevenly in the unfertilized egg
Fig. 18-15a
•
Unfertilized egg cell
These substances include
cytoplasmic determinants,
maternal substances in the
Sperm
Fertilization
egg that influence early development
–
Nucle
Two different
cytoplasmic
determinants
Zygote
As the zygote divides by mitosis,
cells contain different cytoplasmic
Mitotic
cell division
determinants, which lead to
different gene expression
Two-celled
embryo
(a) Cytoplasmic determinants in the egg
Induction
•
The other important source of developmental information is the environment around
the cell, especially signals from nearby embryonic cells
–
In the process called induction, signal molecules from embryonic cells cause
transcriptional changes in nearby target cells
•
Gene expression is therefore altered in these cells
Fig. 18-15b
•
Thus, interactions between cells
induce differentiation of
specialized cell types
Early embryo
(32 cells)
Signal
transduction
pathway
Signal
receptor
Signal
molecule
(inducer)
Animation: Cell Signaling
(b) Induction by nearby cells
NUCLEUS
Sequential Regulation of Gene Expression During
Cellular Differentiation
•
The term determination refers to the events that lead to the observable
differentiation of a cell
–
Once a cell has undergone determination, it is irreversibly committed to its final
fate
•
If a committed cell is experimentally placed in another location in the
embryo, it will still differentiate into the cell type that is its normal fate
•
–
Determination precedes differentiation
Observable cellular differentiation is marked by the expression of genes for
tissue-specific proteins
•
These proteins are found only in a specific cell type and give the cell its
characteristic structure and function
Differentiation of Skeletal Muscle Cells
•
We can look at the differentiation of skeletal muscle cells as an example:
–
Muscle cells develop from embryonic precursor cells that have the potential to
develop into a number of cell types, including cartilage and fat cells
–
Once determination occurs, these cells are called myoblasts
•
Myoblasts produce muscle-specific proteins and eventually differentiate to
form skeletal muscle cells
–
MyoD is one of several “master regulatory genes” that produce proteins that
commit the cell to becoming skeletal muscle
•
This gene encodes MyoD protein, a transcription factor that binds to
enhancers of various target genes and stimulates their expression
•
Then, secondary transcription factors activate the genes for proteins such
as myosin and actin that confer the unique properties of skeletal muscle
cells
•
Step 1: Determination - Signals from other cells lead to activation of the master
regulatory gene myoD, allowing the cell to make MyoD protein, which acts as an
activator
–
•
The cell is now called a myoblast and is irreversibly committed to becoming a
skeletal muscle cell
Step 2: Differentiation - MyoD protein stimulates the myoD gene further and
activates genes encoding for other muscle-specific transcription factors
–
–
–
These transcription factors
activate genes for muscle
proteins like myosin and actin
Fig. 18-16-3
MyoD also turns on
genes that block the
cell cycle, thus
stopping cell division
The nondividing
myoblasts fuse to
become mature
multinucleate muscle
cells, also called
muscle fibers
Nucleus
Master regulatory gene myoD
Embryonic
precursor cell
Other muscle-specific genes
DNA
Myoblast
(determined)
OFF
OFF
mRNA
OFF
MyoD protein
(transcription
factor)
mRNA
MyoD
Part of a muscle fiber
(fully differentiated cell)
mRNA
Another
transcription
factor
mRNA
mRNA
Myosin, other
muscle proteins,
and cell cycle–
blocking proteins
Pattern Formation: Setting Up the Body Plan
•
For differentiated cells and tissues to function effectively in the organism as a whole,
the organism’s body plan (its 3-D arrangement) must be established and
superimposed on the differentiation process
–
Pattern formation is the development of a spatial organization of tissues and
organs
•
In animals, pattern formation begins with the establishment of the major
axes
–
The three major axes of a bilaterally symmetrical animal include head
and tail, right and left sides, and back and front
•
The molecular cues that control pattern formation are collectively known as
positional information
– These cytoplasmic determinants and inductive signals tell a cell its
location relative to the body axes and to neighboring cells
Pattern Formation in Drosophila
• Pattern formation has been extensively studied in
the fruit fly Drosophila melanogaster
– Combining anatomical, genetic, and
biochemical approaches, researchers have
discovered developmental principles common
to many other species, including humans
The Life Cycle of Drosophila
•
In Drosophila, cytoplasmic determinants in the unfertilized egg provide
positional information for the placement of anterior-posterior and dorsalventral axes even before fertilization
–
This egg develops in the female’s ovary, surrounded by ovarian cells
called nurse cells and follicle cells
• These support cells supply the egg with nutrients, mRNAs, and
other substances needed for development and make the egg shell
• After fertilization, the embryo develops into a segmented larva with
three larval stages
•
1) The yellow egg is surrounded by other cells that form a structure called the follicle
within one of the mother’s ovaries
•
2)Nurse cells shrink as they supply nutrients and mRNAs to the developing egg,
Fig. 18-17b
which grows larger
Follicle cell
1 Egg cell
Nucleus
developing within
ovarian follicle
–
Eventually, the mature egg fills
Egg
cell
Nurse cell
the egg shell that is secreted by
Egg
shell
2 Unfertilized egg
the follicle cells
•
3)The egg is fertilized within the
mother and then laid
•
Depleted
nurse cells
3 Fertilized egg
Embryonic
development
4-5) Embryonic development forms
a larva that goes through 3 stages
–
The
3rd
4 Segmented
embryo
stage forms a cocoon (not shown), within
which the larva metamorphoses into the
adult shown
Fertilization
Laying of egg
0.1 mm
Body
segments
Hatching
5 Larval stage
(b) Development from egg to larva
Genetic Analysis of Early Development: Scientific
Inquiry
•
Edward B. Lewis, Christiane Nüsslein-Volhard, and Eric Wieschaus won a Nobel
1995 Prize for decoding pattern formation in Drosophila
–
These scientists studied mutant flies with developmental defects that led to
extra wings or legs in the wrong places
•
They located these mutations on the fly’s genetic map, thus connecting
developmental abnormalities to specific genes
Fig. 18-18
–
Their research supplied the first concrete evidence that genes somehow direct
developmental processes
•
These genes that
Eye
control pattern
formation in the late
embryo, larva, and
Leg
Antenna
adult are called
homeotic genes
Wild type
Mutant
•
Thirty years later, Nüsslein-Volhard and Wieschaus set out to identify all the
genes that affect segment formation in Drosophila
–
They created mutants, conducted breeding experiments, and looked for
corresponding genes
• Breeding experiments were complicated by embryonic lethals,
embryos with lethal mutations
–
They found 120 genes essential for normal segmentation
• The researchers were able to group these segmentation genes by
general function, to map them, and to clone many of them for
further study in the lab
Axis Establishment
•
Maternal effect genes encode for cytoplasmic determinants that initially establish
the axes of the body of Drosophila
–
When these genes are mutant in the mother, any offspring display the mutant
phenotype regardless of the offspring’s own genotype
–
These maternal effect genes are also called egg-polarity genes because they
control orientation of the egg and consequently, that of the fly
•
One group of these genes sets up the anterior-posterior axis of the
embryo, while a second group establishes the dorsal-ventral axis
–
Mutations in these maternal effect genes are generally embryonic lethals
Animation: Development of Head-Tail Axis in Fruit Flies
The Bicoid Gene
•
One maternal effect gene, the bicoid gene, affects the front half of the body
–
An embryo whose mother has a mutant bicoid gene lacks the front half of its
body and has duplicate posterior structures at both ends
•
This phenotype suggested that the product of the mother’s bicoid gene is
essential for setting up the anterior end of the fly and therefore might be
concentrated at the future anterior end of the embryo
Fig. 18-19a
•
This hypothesis is an example of the
EXPERIMENT
Tail
morphogen gradient hypothesis, in
Head
which gradients of substances called
T1
morphogens establish an embryo’s axes
and other features of its form
T2
T3
A1 A2
A6
A3 A4 A5
A7
A8
Wild-type larva
Tail
Tail
A8
A8
A7
Mutant larva (bicoid)
A6
A7
•
Experiment: many embryos and larvae with defects in their body patterns were
obtained
–
Some of these defects were due to mutations in the mother’s genes, including
the bicoid (“two-tailed”) gene, which resulted in larvae with two tails and no
head
–
The researchers hypothesized that bicoid normally codes for a morphogen
specifying the head (anterior) end of the embryo
•
•
Results: bicoid mRNA (dark blue)
was confined to the anterior end of the
Fig. 18-19b
unfertilized egg
–
•
To test this hypothesis, they used molecular techniques to determine
where the mRNA and protein encoded by this gene were found in the
fertilized egg and early embryo
Later in development, Bicoid protein was seen to be concentrated in cells at the
anterior end of the embryo
RESULTS
Conclusion: the results support the hypothesis that Bicoid protein is a morphogen
specifying formation of headspecific structures
100 µm
Bicoid mRNA in mature
unfertilized egg
Fertilization,
translation
Anterior end
of bicoid
Bicoid protein in early
mRNA
embryo
Importance of Bicoid Research
•
The bicoid research is important for three reasons:
–
It identified a specific protein required for some early steps in pattern formation
•
This helped us understand how different regions of the egg can give rise to
cells that go down different developmental pathways
–
It increased understanding of the mother’s role in embryo development
–
It demonstrated the key developmental principle that a gradient of molecules
can determine polarity and position in the embryo
•
In Drosophila, gradients of specific proteins determine the posterior and
anterior ends, as well as the dorsal-ventral axis
•
Positional information later establishes a specific number of correctly
oriented segments and triggers the formation of each segment’s
characteristic structures
–
The pattern of the adult is abnormal when the genes operating in this
final step are abnormal
Concept 18.5:
Cancer results from genetic changes
that affect cell cycle control
Cancer and Gene Regulation
•
The gene regulation systems that go wrong during cancer are the very same
systems involved in embryonic development
–
Cancer can be caused by mutations to genes that regulate cell growth
and division
• The agents of these changes can be random spontaneous
mutation, or they may be caused by environmental influences,
including chemical carcinogens and X-rays
• Tumor viruses can also cause cancer in animals, including
humans
– Ex) Human papillomaviruses (HPV) are associated with
cervical cancer
Oncogenes and Proto-Oncogenes
• Oncogenes are cancer-causing genes
– Proto-oncogenes are the corresponding normal cellular
genes that are responsible for normal cell growth and
division
• An oncogene usually arises from a genetic change that
leads to an increase either in the amount of the gene’s
protein product or in the activity of each protein
molecule
– Conversion of a proto-oncogene to an oncogene can
lead to abnormal stimulation of the cell cycle
Conversion of Proto-Oncogenes to Oncogenes
•
Genetic changes that convert proto-oncogenes to oncogenes fall into 3 main
categories:
–
Movement of DNA (translocation) within the genome: if it ends up near an
active promoter, transcription may increase
–
Amplification of a proto-oncogene: increases the number of copies of the protoFig. 18-20
oncogene
in the cell
–
Point mutation in a control element or in the proto-oncogene itself, causing an
increase in gene expression
Proto-oncogene
DNA
Translocation or
transposition:
Point mutation:
Gene amplification:
within a control element
New
promoter
Normal growthstimulating
protein in excess
Oncogene
Normal growth-stimulating
protein in excess
Normal growthstimulating
protein in excess
within the gene
Oncogene
Hyperactive or
degradationresistant protein
Tumor-Suppressor Genes
•
Cells also contain genes known as tumor-suppressor genes whose normal
products inhibit cell division
–
The proteins they encode help prevent uncontrolled cell growth
–
Mutations that decrease protein products of tumor-suppressor genes may
contribute to cancer onset
•
The protein products of tumor-suppressor genes have various functions:
–
Repair damaged DNA, preventing the cell from accumulating cancer-causing
mutations
–
Control adhesion of cells to one another or to the extracellular matrix, which is
crucial in normal tissues and often absent in cancers
–
Inhibit the cell cycle in the cell-signaling pathway
Interference with Normal Cell-Signaling Pathways
• The proteins encoded by many proto-oncogenes and tumorsuppressor genes are components of cell-signaling pathways
– The products of 2 key genes, ras proto-oncogene and the
p53 tumor-suppressor gene, can be examined in order to
elucidate what goes wrong with the functioning of these
proteins in cancer cells
• Mutations in the ras gene can lead to production of a
hyperactive Ras protein and increased cell division
The Ras Protein
•
The Ras (named for rat sarcoma) protein is a G protein that relays a signal
from a growth factor receptor on the plasma membrane to a cascade of
protein kinases
–
The cellular response at the end of the pathway is the synthesis of a
protein that stimulates the cell cycle
• Normally, this pathway will not operate unless triggered by the
appropriate growth factor
• Certain mutations in the ras gene can lead to production of a
hyperactive Ras protein that triggers the kinase cascade even in
the absence of growth factor
– Results in increased cell division
•
The normal cell cycle-stimulating pathway is triggered by a growth factor (1) that
binds to its receptor (2) in the plasma membrane
•
The signal is relayed to a G protein (3) called Ras
–
•
Ras is active when GTP is bound to it
Ras passes the signal to a series of protein kinases (4)
Fig. 18-21a
•
The last kinase (5) activates a
1 Growth
factor
1
MUTATION
Hyperactive
Ras protein
(product of
oncogene)
issues
signals
on its own
Ras
transcription activator that turns on
3 G protein
Ras
one or more genes for proteins that
stimulate the cell cycle
–
Results in excessive
GTP
GTP
2 Receptor
4 Protein kinases
(phosphorylation
cascade)
NUCLEUS
5 Transcription
factor (activator)
cell division that may
DNA
cause cancer
Gene expression
Protein that
stimulates
the cell cycle
(a) Cell cycle–stimulating pathway
The p53 Gene
•
If the DNA of a cell is damaged, another signaling pathway blocks the cell cycle until
the damage has been repaired
–
Thus, the genes for components of this pathway act as tumor-suppressor
genes
•
One is these genes, called the p53 gene, encodes a specific transcription
factor that promotes the synthesis of cell cycle-inhibiting proteins
–
Activates a gene called p21 whose product halts the cell cycle by
binding to cyclin-dependent kinases, thus allowing time for DNA repair
–
Also turns on genes directly involved in DNA repair
–
When DNA damage is irreparable, p53 activates “suicide genes”
whose proteins cause cell death by apoptosis
•
A mutation that knocks out the p53 gene can lead to excessive cell growth
and cancer
•
In the normal cell cycle-inhibiting pathway, DNA damage (1) is an
intracellular signal that is passed via protein kinases (2) and leads to
activation of p53 (3)
–
Activated p53 promotes transcription of the gene for a protein that
inhibits the cell cycle
Fig. 18-21b
• This suppression ensures that damaged DNA is not replicated
2 Protein kinases
MUTATION
3 Active
form
of p53
UV
light
1 DNA damage
in genome
DNA
Protein that
inhibits
the cell cycle
(b) Cell cycle–inhibiting pathway
Defective or
missing
transcription
factor, such
as p53, cannot
activate
transcription
Fig. 18-21
1 Growth
factor
MUTATION
Hyperactive
Ras protein
(product of
oncogene)
issues
signals
on its own
Ras
•
Mutations causing deficiencies in
3 G protein
GTP
Ras
any pathway component can
contribute to the development
GTP
2 Receptor
4 Protein kinases
(phosphorylation
cascade)
NUCLEUS
5 Transcription
factor (activator)
of cancer
DNA
–
Gene expression
Increased cell division that
Protein that
stimulates
the cell cycle
may lead to cancer can
(a) Cell cycle–stimulating pathway
result if the cell cycle is
2 Protein kinases
MUTATION
over-stimulated via the
cell cycle-stimulating
pathway (a)
–
3 Active
form
of p53
UV
light
1 DNA damage
in genome
A similar effect can be seen
Defective or
missing
transcription
factor, such
as p53, cannot
activate
transcription
DNA
Protein that
inhibits
the cell cycle
if the mutation affects the
(b) Cell cycle–inhibiting pathway
cell cycle-inhibiting
pathway (b)
EFFECTS OF MUTATIONS
Protein
overexpressed
Cell cycle
overstimulated
Protein absent
Increased cell
division
Cell cycle not
inhibited
The Multistep Model of Cancer Development
• Multiple mutations are generally needed for full-fledged cancer
– The longer we live, the more mutations we accumulate
• This may help explain why the incidence of cancer
increases greatly with age
– At the DNA level, a cancerous cell is usually characterized
by at least one active oncogene and the mutation of
several tumor-suppressor genes
•
The model of a multistep path to cancer is well-supported by studies of colorectal
cancer
–
–
Like most cancers, colorectal cancer develops gradually
•
The 1st sign is often a polyp, made up of cells that look normal but divide
unusually frequently
•
The tumor grows and may eventually become malignant, spreading to
other tissues
The
development of this malignant tumor is caused by a gradual accumulation
Fig. 18-22
of mutations that convert proto-oncogenes to oncogenes and knock out tumorsuppressor genes
•
A ras oncogene and a mutated p53 tumor-suppressor gene are often
involved
Colon
EFFECTS OF MUTATIONS
1 Loss of tumorsuppressor
gene
Colon wall
APC (or other)
Normal colon
epithelial cells
Small benign
growth (polyp)
2 Activation of
ras oncogene
4 Loss of
tumor-suppressor
gene p53
3 Loss of
tumor-suppressor
gene DCC
5 Additional
mutations
Larger benign
growth (adenoma)
Malignant tumor
(carcinoma)
Inherited Predisposition and Other Factors
Contributing to Cancer
• Individuals can inherit oncogenes or mutant alleles of
tumor-suppressor genes
– Inherited mutations in the tumor-suppressor gene
adenomatous polyposis coli are common in
individuals with colorectal cancer
– Mutations in the BRCA1 or BRCA2 gene are found
in at least half of inherited breast cancers
You should now be able to:
1. Explain the concept of an operon and the
function of the operator, repressor, and
corepressor
2. Explain the adaptive advantage of grouping
bacterial genes into an operon
3. Explain how repressible and inducible operons
differ and how those differences reflect
differences in the pathways they control
4. Explain how DNA methylation and histone
acetylation affect chromatin structure and the
regulation of transcription
5. Define control elements and explain how they
influence transcription
6. Explain the role of promoters, enhancers,
activators, and repressors in transcription
control
7. Explain how eukaryotic genes can be
coordinately expressed
8. Describe the roles played by small RNAs on
gene expression
9. Explain why determination precedes
differentiation
10. Describe two sources of information that
instruct a cell to express genes at the
appropriate time
11. Explain how maternal effect genes affect
polarity and development in Drosophila
embryos
12. Explain how mutations in tumor-suppressor
genes can contribute to cancer
13. Describe the effects of mutations to the p53
and ras genes