biochemistry regulation of gene expression
TRANSCRIPT
Lecture 26
Regulation of gene expression
Signal
NUCLEUSChromatin
Chromatin modification:DNA unpacking involvinghistone acetylation and
DNA demethylationDNA
Gene
Gene availablefor transcription
RNA ExonPrimary transcript
Transcription
Intron
Cap
Tail
mRNA in nucleus
Transport to cytoplasm
CYTOPLASM
mRNA in cytoplasm
TranslationDegradationof mRNA
Polypeptide
Protein processing, suchas cleavage and
chemical modification
Active proteinDegradation
of proteinTransport to cellular
destination
Cellular function (suchas enzymatic activity,structural support)
Overview• Prokaryotes and eukaryotes alter gene expression in
response to their changing environment• In multicellular eukaryotes, gene expression regulates
development and is responsible for differences in cell types
• RNA molecules play many roles in regulating gene expression in eukaryotes
Regulation of gene expression
in prokaryotic cell - Operon units, system of
negative feedback
in eukaryotic cell come at any stage of gene
expression and proteosynthesis. Important are
noncoding RNAs.
Bacteria often respond to environmental change by regulating
transcription• Natural selection has favored bacteria that produce only
the products needed by that cell• A cell can regulate the production of enzymes by
feedback inhibition or by gene regulation• Gene expression in bacteria is controlled by the operon
model
Precursor
Feedbackinhibition
Enzyme 1
Enzyme 2
Enzyme 3
Tryptophan
Regulation of enzymeactivity
Regulation of enzymeproduction
Regulationof geneexpression
trpE gene
trpD gene
trpC gene
trpB gene
trpA gene
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• An operon is the entire stretch of DNA that includes
the operator, the promoter, and the genes that they control
Operon is a functional unit common in bacteria and phages. Activation
and inhibition of transcription are regulated in response of conditions
in environment.
Prokaryotic genetic information is not divided into introns and exons.
Operon
• is coordinately regulated clusters of genes,
which are transcribed into one mRNA
(polygenic mRNA)
• are genes for particular metabolic pathway
and are regulated by common promoter and
are ordered on DNA following each other
Escherichia coli
Lac operon, Trp operon – model systems =
metabolic pathways of
• utilization of lactose gen lacZ, lacY, lacA, catabolic
pathway with negative and positive regulation
• enzymes for TRP synthesis, anabolic pathway
with negative regulation
• The operon can be switched off by a protein repressor• The repressor prevents gene transcription by binding to
the operator and blocking RNA polymerase• The repressor can be in an active or inactive form,
depending on the presence of other molecules• A corepressor is a molecule that cooperates with a
repressor protein to switch an operon off• For example, E. coli can synthesize the amino acid
tryptophan
• By default the trp operon is on and the genes for tryptophan synthesis are transcribed
• 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; thus the trp operon is turned off (repressed) if tryptophan levels are high
Promoter
DNA
Regulatory gene
mRNA
trpR
5
3
Protein Inactive repressor
RNApolymerase
Promoter
trp operon
Genes of operon
Operator
mRNA 5
Start codon Stop codon
trpE trpD trpC trpB trpA
E D C B A
Polypeptide subunits that make upenzymes for tryptophan synthesis
(a) Tryptophan absent, repressor inactive, operon on
(b) Tryptophan present, repressor active, operon off
DNA
mRNA
Protein
Tryptophan (corepressor)
Activerepressor
No RNAmade
Repressible and Inducible Operons: Two Types of Negative Gene Regulation
• A repressible operon is one that is usually on; binding of a repressor to the operator shuts off transcription
• The trp operon is a repressible operon• An inducible operon is one that is usually off; a
molecule called an inducer inactivates the repressor and turns on transcription
• The lac operon is an inducible operon and contains genes that code for enzymes used in the hydrolysis and metabolism of lactose
• By itself, the lac repressor is active and switches the lac operon off
• A molecule called an inducer inactivates the repressor to turn the lac operon on
(a) Lactose absent, repressor active, operon off
(b) Lactose present, repressor inactive, operon on
Regulatorygene
Promoter
Operator
DNA lacZlacI
lacI
DNA
mRNA5
3
NoRNAmade
RNApolymerase
ActiverepressorProtein
lac operon
lacZ lacY lacADNA
mRNA
5
3
Protein
mRNA 5
Inactiverepressor
RNA polymerase
Allolactose(inducer)
-Galactosidase Permease Transacetylase
Lac operon - negative regulation
• regulatory gene produces repressor, which
binds operator and causes that RNAP is not
able to initialize transcription
• in the presence of lactose repressor is released
from operator. The repressor is changed by
inducer / lactoseRNA polymerase starts the transcription. In 2-3 minutes the amount of
enzymes is increased 1000x
• Inducible enzymes usually function in catabolic pathways; their synthesis is induced by a chemical signal
• Repressible enzymes usually function in anabolic pathways; their synthesis is repressed by high levels of the end product
• Regulation of the trp and lac operons involves negative control of genes because operons are switched off by the active form of the repressor
Positive Gene Regulation
• Some operons are also subject to positive control through a stimulatory protein, such as catabolite activator protein (CAP), an activator of transcription
• When glucose (a preferred food source of E. coli) is scarce, CAP is activated by binding with cyclic AMP (cAMP)
• Activated CAP attaches to the promoter of the lac operon and increases the affinity of RNA polymerase, thus accelerating transcription
• In the presence of glucose, E. coli preferentially uses
glucose for decomposing.
• If is low level of glucosis, the cAMP is increased.
• CAP (Catabolite activator protein) in the presence
of cAMP attaches promoter and activates the
transcription.
• CAP is allosteric regulatory protein• When glucose levels increase, CAP detaches from the
lac operon, and transcription returns to a normal rate
Lac operon - positive regulation
Promoter
DNA
CAP-binding site
lacZlacI
RNApolymerasebinds andtranscribes
Operator
cAMPActiveCAP
InactiveCAP
Allolactose
Inactive lacrepressor
(a) Lactose present, glucose scarce (cAMP level high):abundant lac mRNA synthesized
Promoter
DNA
CAP-binding site
lacZlacI
OperatorRNApolymerase lesslikely to bind
Inactive lacrepressor
InactiveCAP
(b) Lactose present, glucose present (cAMP level low):little lac mRNA synthesized
Summary
each operon consists of • promoter (for RNA polymerase)• operator (for repressor)• several structural genes• terminator
repressor = allosteric protein encoded by regulatory gene
co-repressor = product moleculeinducer = substrate molecule
Eukaryotic gene expression is regulated at many stages
• All organisms must regulate which genes are expressed at any given time
• In multicellular organisms regulation of gene expression is essential for cell specialization
Gene expression of eukaryotic cells
• each cell maintains specific program /
differential gene expression
• one mRNA carries information for one gene
(monogennic mRNA)
• posttranscription modifications of RNA
RNA processing and splicing
• regulation system is performed at the several
levels = transcription, translation, protein
activation + secretion
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
• Abnormalities in gene expression can lead to diseases including cancer
• Gene expression is regulated at many stages
Signal
NUCLEUSChromatin
Chromatin modification:DNA unpacking involvinghistone acetylation and
DNA demethylationDNA
Gene
Gene availablefor transcription
RNA ExonPrimary transcript
Transcription
Intron
Cap
Tail
mRNA in nucleus
Transport to cytoplasm
CYTOPLASM
mRNA in cytoplasm
TranslationDegradationof mRNA
Polypeptide
Protein processing, suchas cleavage and
chemical modification
Active proteinDegradation
of proteinTransport to cellular
destination
Cellular function (suchas enzymatic activity,structural support)
Many steps at which eucaryotic gene expression can be controlled
• chromatin changes
• transcription
• processing RNA
• transport to cytoplasm
• degradation of mRNA
• translation
• cleavage, chemical modification
• protein degradation
more complicated regulating system
• Heterochromatin is highly condensed that is why
transcriptional enzymes can not reach the DNA
• Acetylation / deacetylation of histons
• Methylation [cytosin] - inactive DNA is highly
methylated
DNA methylation and histone de-acetylation repress
the transcription.
1. Chromatin changes
• DNA methylation
is esential for long-term inactivation of genes during
cell differentiation
Gene imprinting in mamals
• methylation constantly turns off the maternal or the
paternal allele of a gene in early development
• certain genes are expressed in a parent-of-origin-
specific manner
Epigenetic inheritance
Histone Modifications• In histone acetylation, acetyl groups are attached to
positively charged lysines in histone tails• This loosens chromatin structure, thereby promoting the
initiation of transcription• The addition of methyl groups (methylation) can
condense chromatin; the addition of phosphate groups (phosphorylation) next to a methylated amino acid can loosen chromatin
Amino acidsavailablefor chemicalmodification
Histone tails
DNA double helix
Nucleosome(end view)
(a) Histone tails protrude outward from a nucleosome
Unacetylated histones Acetylated histones
(b) Acetylation of histone tails promotes loose chromatinstructure that permits transcription
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
• In genomic imprinting, methylation regulates expression of either the maternal or paternal alleles of certain genes at the start of development
Epigenetic Inheritance• Although the chromatin modifications just discussed 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
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
2. Transcription
Transcription factors:
proteins that bind DNA and facilitate or inhibit RNA
polymerase to bind. They are a part of transcription initiation
complex.
general transcription factors for all protein-coding genes
specific transcription factors – transcription of particular
genes at appropriate time and place
- enhancers, activators, inhibitors, repressors
Organization of a Typical Eukaryotic Gene
• 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 are critical to the precise regulation of gene expression in different cell types
Enhancer(distal control
elements)
DNA
UpstreamPromoter
Proximalcontrol
elementsTranscription
start site
Exon Intron Exon ExonIntron
Poly-Asignal
sequenceTranscriptiontermination
region
DownstreamPoly-Asignal
Exon Intron Exon ExonIntron
Transcription
Cleaved3 end ofprimarytranscript
5Primary RNAtranscript(pre-mRNA)
Intron RNA
RNA processing
mRNA
Coding segment
5 Cap 5 UTRStart
codonStop
codon 3 UTR
3
Poly-Atail
PPPG AAA AAA
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
• 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
Enhancers and Specific Transcription Factors
• An activator is a protein that binds to an enhancer and stimulates transcription of a gene
• Activators have two domains, one that binds DNA and a second that activates transcription
• Bound activators facilitate a sequence of protein-protein interactions that result in transcription of a given gene
• 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
ActivatorsDNA
EnhancerDistal controlelement
PromoterGene
TATA box
Generaltranscriptionfactors
DNA-bendingprotein
Group of mediator proteins
RNApolymerase II
RNApolymerase II
RNA synthesisTranscriptioninitiation complex
Cell-type specific transcription:
Genes encoding the enzymes of one metabolic
pathway are scattered over the different
chromosomes - coordinated control in
response of chemical signals from outside
the cell. The cell accept signals by receptors.
Signal transduction pathways activate
transcription activators or repressors.
Signal transduction pathways
Controlelements
Enhancer Promoter
Albumin gene
Crystallingene
LIVER CELLNUCLEUS
Availableactivators
Albumin geneexpressed
Crystallin genenot expressed
(a) Liver cell
LENS CELLNUCLEUS
Availableactivators
Albumin genenot expressed
Crystallin geneexpressed
(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
Nuclear Architecture and Gene Expression
• Loops of chromatin extend from individual chromosomes into specific sites in the nucleus
• Loops from different chromosomes may congregate at particular sites, some of which are rich in transcription factors and RNA polymerases
• These may be areas specialized for a common function
Chromosometerritory
Chromosomes in theinterphase nucleus
Chromatinloop
Transcriptionfactory
10 m
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
Exons
DNA
Troponin T gene
PrimaryRNAtranscript
RNA splicing
ormRNA
1
1
1 1
2
2
2 2
3
3
3
4
4
4
5
5
5 5
• 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
3. Processing RNA
• 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
• Nucleotide sequences that influence the lifespan of mRNA in eukaryotes reside in the untranslated region (UTR) at the 3 end of the molecule
4, 5. transport of mRNA / degradation
6. Translation
At the initiation stage – regulatory proteins bind the
5’ end of the mRNA with the cap.
Activation or inactivation of protein factors to initiate
translation
7. Cleavage, chemical modifications
Cleavage
Post-translational modifications
Regulatory proteins [products] are activated
or inactivated by the reversible addition of
phosphate groups / phosphorylation
Sugars on surface of the cell / Glycosylation
• Polypeptide chain may
be cleaved into two or
three pieces
• Preproinsulin
• Proinsulin - disulfide
bridges
• Insulin
• Secretory protein
Acid/base - act/inact
Hydrolysis – localization, act/inact
Acetylation - act/inact
Phosphorylation - act/inact
Prenylation - localization
Glycosylation - targeting
Post-translational modifications
• Lifespan of protein is strictly regulated• 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.
8. protein degradation
Chromatin modification
• Genes in highly compactedchromatin are generally nottranscribed.• Histone acetylation seemsto loosen chromatin structure,enhancing transcription.
• DNA methylation generallyreduces transcription.
mRNA degradation
• Each mRNA has a characteristic life span,determined in part bysequences in the 5 and3 UTRs.
• Regulation of transcription initiation:DNA control elements in enhancers bindspecific transcription factors.
Bending of the DNA enables activators tocontact proteins at the promoter, initiatingtranscription.
• Coordinate regulation:Enhancer for
liver-specific genesEnhancer for
lens-specific genes
Transcription
RNA processing
• Alternative RNA splicing:
Primary RNAtranscript
mRNA or
• Initiation of translation can be controlledvia regulation of initiation factors.
• Protein processing anddegradation by proteasomesare subject to regulation.
Translation
Protein processing and degradation
Chromatin modification
Transcription
RNA processing
mRNAdegradation
Translation
Protein processingand degradation
Example of gene regulation
Regulation & DevelopmentRegulation & Development
• hox Geneshox Genes– Control Organ & Tissue Development Control Organ & Tissue Development
In The EmbryoIn The Embryo
– Mutations Lead To Major ChangesMutations Lead To Major Changes• Drosophila With Legs In Place of Drosophila With Legs In Place of
AntennaeAntennae
Regulation & DevelopmentRegulation & Development
Regulation & DevelopmentRegulation & Development
hox Geneshox Genes Present In All EukaryotesPresent In All Eukaryotes– Shows Common AncestryShows Common Ancestry
– Pax 6 hox genePax 6 hox gene• Controls eye growth in Drosophila, Mice & Controls eye growth in Drosophila, Mice &
ManMan
• Pax 6Pax 6 from Mouse Placed In Knee from Mouse Placed In Knee Development Sequence Of Drosophila Development Sequence Of Drosophila Developed Into Eye Tissue.Developed Into Eye Tissue.
Common Ancestor >600M Years AgoCommon Ancestor >600M Years Ago
Homeotic mutations transform one body part into another.
Wild type Mutant
Eye
AntennaLeg
The Regulation of Eukaryotic Gene Expression
..using the example of PEPCK
PEPCK
• This is an acronym for an enzyme• PhosphoEnol Pyruvate CarboxyKinase• This enzyme is ONLY regulated by gene
expression!• No allosteric activators, covalent
modification etc• No activation by cAMP, inhibition by insulin
etc
PEPCK
• The enzyme is expressed in liver, kidney, adipose tissue and to a lesser extent in muscle
• It is a key enzyme in gluconeogenesis (the synthesis of new glucose, usually from lactate, pyruvate or alanine) and glyceroneogenesis (the synthesis of glycerol, usually from lactate, pyruvate or alanine)
PEPCK overexpression in muscle
• a mouse with PEPCK overexpressed in muscle only.
• This mouse was leaner than wild type mice, ran for longer and lived longer!
• They were also more aggressive.
• The overexpression had switched the muscle fuel usage to fatty acids with little lactate production.
The Supermouse….
• Eats 60% more food than wild type mice
• Weighs 40% less than wild type mice
• Can run for >4 h until exhaustion whereas the control littermates stop after only 10 min
• Has 2 – 3 fold less adipose tissue
PEPCK overexpression in adipose tissue
• A mouse has the PEPCK enzyme overexpressed in adipose tissue.
• The results couldn’t be further from supermouse!
PEPCK overexpression in fat cells
PEPCK overexpression in adipose tissue
• These mice are obese although metabolically healthy (as measured by glucose
tolerance and insulin sensitivity) until you put them on a high fat diet.
• Then you see insulin resistance and diabetes emerging.
PEPCK overexpression in liver
• Leads to altered glucose tolerance
• Insulin resistance
• Increased gluconeogenesis causes increased hepatic glucose production which is released into the blood stream
• This caused increased insulin secretion but ultimately insulin resistance.
PEPCK Knock out in liver
• Surprisingly these mice can maintain blood glucose under starvation conditions
• They develop liver steatosis (fatty livers) probably because of impaired oxidation of fatty acids
• A total PEPCK knock out in all tissues is lethal…mice die within days of birth.
Why the dramatically different outcome for the mouse when PEPCK is overexpressed in different tissues?It is after all the same enzyme catalysing
the same reaction.
Glyceroneogenesis
PEPcarboxykinase
COOH
C
CH2
O
CO
H2C COOH
COOH
oxaloacetateOAA
PO3
Phosphoenol pyruvatePEP
COOH
C O
CH3
COOH
HC OH
CH3
NADH NAD+
Pyruvate Lactate
CO2
Pyruvate Carboxylase LDH
CO2
GTP
GDPAlanine
Glyceroneogenesis
CH2OPO3
C O
CH2OH
CH2OPO3
HC OH
C
O
Glyceraldehyde 3-P
Dihydroxyacetone phosphate (DHAP)
H
CH2OPO3
HC OH
CH2OH
Glycerol 3-P
Triglycerides
Fatty acids H3C CO
S-CoA
PEP