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