Regulation of Gene Expression
From: University of Wisconsin, Department of Biochemistry
Potential Points for the Regulation of Gene Expression
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 gene regulation
• Gene expression in bacteria is controlled by the operon model
Prokaryotes
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 (lac operon )
Transcriptional Control
Fig. 18-3a
Polypeptide subunits that make upenzymes for tryptophan synthesis
Tryptophan absent, repressor inactive, operon on
DNA
mRNA 5
Protein Inactiverepressor
RNApolymerase
Regulatorygene
Promoter Promoter
trp operon
Genes of operon
OperatorStop codonStart codon
mRNA
trpA
5
3
trpR trpE trpD trpC trpB
ABCDE
The trp operon is a repressible operon
Fig. 18-3b-1
Tryptophan present, repressor active, operon off
Tryptophan(corepressor)
No RNA made
Activerepressor
mRNA
Protein
DNA
Fig. 18-3b-2
(b) Tryptophan present, repressor active, operon off
Tryptophan(corepressor)
No RNA made
Activerepressor
mRNA
Protein
DNA
• 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
The lac operon is inducible.
Fig. 18-4a
DNA
Protein Activerepressor
RNApolymerase
Regulatorygene
Promoter
Operator
mRNA5
3
NoRNAmade
lacI lacZ
Lactose absent, repressor active, operon off
Fig. 18-4b
Lactose present, repressor inactive, operon on
mRNA
Protein
DNA
mRNA 5
Inactiverepressor
Allolactose(inducer)
5
3
RNApolymerase
Permease Transacetylase
lac operon
-Galactosidase
lacYlacZ lacAlacI
• 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
Fig. 18-5
cAMP
DNA
Inactive lacrepressor
Allolactose
InactiveCAP
lacI
CAP-binding site
Promoter
ActiveCAP
Operator
lacZRNApolymerasebinds andtranscribes
Inactive lacrepressor
lacZ
OperatorPromoter
DNA
CAP-binding site
lacI
RNApolymerase lesslikely to bind
InactiveCAP
Lactose present, glucose present (cAMP level low): little lac mRNA synthesized
Lactose present, glucose scarce (cAMP level high): abundant lac mRNA synthesized
CAP interaction with cAMP animation
Organization of a Typical Eukaryotic Gene
• Associated with most eukaryotic genes are control elements, segments of noncoding DNA that help regulate transcription by binding certain proteins
• Control elements and the proteins they bind are critical to the precise regulation of gene expression in different cell types
James Darnell chats briefly about signal molecules
Fig. 18-8-1
Enhancer(distal control elements)
Proximalcontrol elements
Poly-A signalsequence
Terminationregion
DownstreamPromoter
UpstreamDNA
ExonExon ExonIntron Intron
Organization of a Typical Eukaryotic Gene
Control elements are segments of noncoding DNA that help regulate transcription by binding certain proteins
HHMI transcription factor interaction animation
Fig. 18-8-2
Enhancer(distal control elements)
Proximalcontrol elements
Poly-A signalsequence
Terminationregion
DownstreamPromoter
UpstreamDNA
Exon Exon ExonIntronIntron Cleaved 3 endof primarytranscript
Primary RNAtranscript
Poly-Asignal
Transcription
5
ExonExon ExonIntron Intron
Fig. 18-8-3
Enhancer(distal control elements)
Proximalcontrol elements
Poly-A signalsequence
Terminationregion
DownstreamPromoter
UpstreamDNA
ExonExon ExonIntron Intron
Exon Exon ExonIntronIntron Cleaved 3 endof primarytranscript
Primary RNAtranscript
Poly-Asignal
Transcription
5 RNA processing
Intron RNA
Coding segment
mRNA
5 Cap 5 UTRStart
codonStop
codon 3 UTR Poly-Atail
3
A Transcription Factor Protein Binds to DNA
Transcription factors recognize particular nucleotide sequences:
NFATs (nuclear factors of activated T cells) are transcription factors that control genes in the immune system.
They bind to a recognition sequence near the genes’ promoters.
The binding produces an induced fit—the protein changes conformation.
How single molecules moveanimation
Fig. 18-9-1 Enhancer TATAbox
PromoterActivators
DNAGene
Distal controlelement
An activator is a protein that binds to an enhancer and stimulates transcription of a gene
Fig. 18-9-2
Enhancer TATAbox
PromoterActivators
DNAGene
Distal controlelement
Group ofmediator proteins
DNA-bendingprotein
Generaltranscriptionfactors
Bound activators cause mediator proteins to interact with proteins at the promoter
Transcription factors act at eukaryotic promoters.
Fig. 18-9-3
Enhancer TATAbox
PromoterActivators
DNAGene
Distal controlelement
Group ofmediator proteins
DNA-bendingprotein
Generaltranscriptionfactors
RNApolymerase II
RNApolymerase II
Transcriptioninitiation complex RNA synthesis
Fig. 18-10
Controlelements
Enhancer
Availableactivators
Albumin gene
(b) Lens cell
Crystallin geneexpressed
Availableactivators
LENS CELLNUCLEUS
LIVER CELLNUCLEUS
Crystallin gene
Promoter
(a) Liver cell
Crystallin genenot expressed
Albumin geneexpressed
Albumin genenot expressed
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
• Some other processes promoting differential gene expression:– Histone modification– DNA methylation
Eukaryotes
A chromosome consists of a DNA molecule packed together with
proteins
© 2011 Pearson Education, Inc.
DNA double helix(2 nm in diameter)
DNA, the double helix
Nucleosome(10 nm in diameter)
Histones
Histones
Histonetail
H1
Nucleosomes, or “beads ona string” (10-nm fiber)
Figure 16.22b
30-nm fiber
30-nm fiber
Loops Scaffold
300-nm fiber
Chromatid(700 nm)
Replicatedchromosome(1,400 nm)
Looped domains(300-nm fiber) Metaphase
chromosome
Histonetails
DNAdouble helix
(a) Histone tails protrude outward from a nucleosome
Acetylated histones
Aminoacidsavailablefor chemicalmodification
(b) Acetylation of histone tails promotes loose chromatin structure that permits transcription
Unacetylated histones
Histone Modifications
In histone acetylation, acetyl groups are attached to positively chargedlysines in histone tails
DNA methylation, the addition of methyl groups to certain bases in DNA, is associated with reduced transcription in some species
DNA Methylation: An Epigenetic Change
•Methylated DNA binds proteins that are involved in repression of transcription—genes tend to be inactive (silenced).
•Patterns of DNA methylation may include large regions or whole chromosomes.
Effects of DNA Methylation:
A Barr body is the transcriptionally inactive X chromosome
A Barr body consists of heavily methylated DNA
Summary: Epigenetic Inheritance• Chromatin modifications do not alter DNA sequence, but 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
• Monozygotic twins show different DNA methylation patterns after living in different environments.
From: The Proceedings of the National Academy of Sciences:The image shows methylation patterns for three-year-old twins (left) and 50-year-old twins (right), with the differences highlighted in red.
or
RNA splicing
mRNA
PrimaryRNAtranscript
Troponin T gene
Exons
DNA
Alternative RNA Splicing
mRNA Degradation
• Nucleotide sequences that influence the lifespan of mRNA in eukaryotes reside in the untranslated region (UTR) at the 3 end of the molecule
Noncoding RNAs play multiple roles in controlling gene expression
• Only a small fraction 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 and chromatin configuration
Micro RNAs (miRNAs)
Figure 19.9
5
Degradation of mRNAOR
Blockage of translation
Target mRNA
miRNA
Proteincomplex
Dicer
Hydrogenbond
The micro-RNA (miRNA)precursor foldsback on itself,held togetherby hydrogenbonds.
12 An enzymecalled Dicer movesalong the double-stranded RNA, cutting it intoshorter segments.
2 One strand ofeach short double-stranded RNA isdegraded; the otherstrand (miRNA) thenassociates with acomplex of proteins.
3 The boundmiRNA can base-pairwith any targetmRNA that containsthe complementarysequence.
4 The miRNA-proteincomplex prevents geneexpression either bydegrading the targetmRNA or by blockingits translation.
5
Small single-stranded RNA molecules that can bind to mRNAdegrading it or blocking its translation
MicroRNA animation (NATURE)
Proteasomeand ubiquitinto be recycledProteasome
Proteinfragments(peptides)Protein entering a
proteasome
Ubiquitinatedprotein
Protein tobe degraded
Ubiquitin
Protein Processing and Degradation
Proteasomes are giant protein complexes that bind protein molecules and degrade them
The length of time a protein functions before it is degraded is strictly regulated.
HHMI Animation
Fig. 18-UN4
• Genes in highly compactedchromatin are generally nottranscribed.
Chromatin modification
• DNA methylation generallyreduces transcription.
• Histone acetylation seems toloosen chromatin structure,enhancing transcription.
Chromatin modification
Transcription
RNA processing
TranslationmRNAdegradation
Protein processingand degradation
mRNA degradation
• Each mRNA has acharacteristic life span,determined in part bysequences in the 5
and3 UTRs.
• Protein processing anddegradation by proteasomesare subject to regulation.
Protein processing and degradation
• Initiation of translation can be controlledvia regulation of initiation factors.
Translation
ormRNA
Primary RNAtranscript
• Alternative RNA splicing:
RNA processing
• Coordinate regulation:
Enhancer forliver-specific genes
Enhancer forlens-specific genes
Bending of the DNA enables activators tocontact proteins at the promoter, initiatingtranscription.
Transcription
• Regulation of transcription initiation:DNA control elements bind specifictranscription factors.
What about cell differentiation and
differential gene expression?
During embryonic development, a fertilized egg gives rise to many different cell types
(a) Cytoplasmic determinants in the egg
Unfertilized egg
Sperm
Fertilization
Zygote(fertilized egg)
Mitoticcell division
Two-celledembryo
Nucleus
Molecules of twodifferent cytoplasmicdeterminants
How do tissues develop?
Interactions between cells induce differentiation of specialized cell types
Induction: signal molecules from embryonic cells cause transcriptional changes in nearby target cells
Induction by nearby cells
Early embryo(32 cells)
NUCLEUSSignaltransductionpathway
Signalreceptor
Signalingmolecule(inducer)
GHOSTS
Sequential Regulation of Gene Expression During Cellular Differentiation
• Determination commits a cell to its final fate• Determination precedes differentiation• Cell differentiation is marked by the production of
tissue-specific proteins
Fig. 18-16-1
Embryonicprecursor cell
Nucleus
OFF
DNA
Master regulatory gene myoD Other muscle-specific genes
OFF
Fig. 18-16-2
Embryonicprecursor cell
Nucleus
OFF
DNA
Master regulatory gene myoD Other muscle-specific genes
OFF
OFFmRNA
MyoD protein(transcriptionfactor)
Myoblast(determined)
Fig. 18-16-3
Embryonicprecursor cell
Nucleus
OFF
DNA
Master regulatory gene myoD Other muscle-specific genes
OFF
OFFmRNA
MyoD protein(transcriptionfactor)
Myoblast(determined)
mRNA mRNA mRNA mRNA
Myosin, othermuscle proteins,and cell cycle–blocking proteinsPart of a muscle fiber
(fully differentiated cell)
MyoD Anothertranscriptionfactor
DNA Methylation: An Epigenetic Change
Many Prokaryotic Genes Are Regulated in Operons
• Sigma factors—other proteins that bind to RNA polymerase and direct it to specific promoters