Chapter 16:Regulation of Gene Expression

2017. 6. 8.생화학교실 장원희

의예1 생물학 I

by David Sinclair

16 Regulation of Gene Expression

1. How Do Viruses Regulate Their Gene Expression?

2. How Is Gene Expression Regulated in Prokaryotes?

3. How Is Eukaryotic Gene Transcription Regulated?

4. How Do Epigenetic Changes Regulate Gene Expression?

5. How Is Eukaryotic Gene Expression Regulated After Transcription?

16.1 How Do Viruses Regulate Their Gene Expression?

Gene expression begins at the promoter where transcription is initiated.

In selective gene transcription, a “decision” is made about which genes to activate.

Two types of regulatory proteins may bind DNA —repressor proteins and activator proteins.

Negative regulation—Gene is normally transcribed; binding of a repressor protein prevents transcription.

Positive regulation—Gene is not normally transcribed; an activator protein binds to stimulate transcription.

Figure 16.1 Positive and Negative Regulation

16.1 How Do Viruses Regulate Their Gene Expression?

The lytic cycle is a typical viral reproductive cycle —the host cell lyses and releases virus particles.

A phage injects a host cell with nucleic acid that takes over the host’s synthetic machinery.

New phage particles appear rapidly and are soon released from the lysed cell.

Figure 16.2 Bacteriophage and Host

16.1 How Do Viruses Regulate Their Gene Expression?

The reproductive cycle of a lytic virus has two stages:

• Early stage — host RNA polymerase binds to promoter in the viral genome and adjacent viral genes are transcribed.

Early genes may shut down host transcription and stimulate viral replication and transcription of viral late genes.

Viral nucleases digest the host’s chromosome for synthesis of viral genomes.

• Late stage — viral late genes are transcribed.

They encode the viral capsid proteins and enzymes to lyse the host cell and release new virions.

The whole process from binding and infection to release of new particles takes about 30 minutes

Figure 16.3 The Lytic Cycle: A Strategy for Viral Reproduction

Figure 16.4 The Lytic and Lysogenic Cycles of Bacteriophage

Some bacteriophage have evolved a process called lysogenythat delays the lytic cycle.

Viral DNA integrates with the host DNA to form a prophage.As the host cell divides, the viral DNA replicates too and can

last for thousands of cycles.

16.1 How Do Viruses Regulate Their Gene Expression?

A kind of genetic switch senses the host’s condition; two regulatory proteins — cI and Cro — compete for promoters on the phage DNA.

The two promoters control viral gene transcription and the regulatory proteins have opposite effects on each promoter.

The two regulatory proteins are made early in phage infection and it is a “race” between them.

If a host cell is not growing well, the virus may switch to the lytic cycle. If growth is slow, Cro is higher and genes for lysis are activated.

In a rapidly growing host, cl synthesis is high and Cro is low — the phage enters a lysogenic cycle.

Figure 16.5 Control of Bacteriophage Lysis and Lysogeny

CIII

host protease FtsH

CII

CI Cro

Lysogenic cycle Lytic cycle

숙주 한 마리에 많은 bacteriophage 감염 (high MOI)

(숙주적다, 영양분에대한숙주간경쟁적다,

숙주가잘자란다숙주에얹혀있는것이유리)

초기 CIII 발현량많음 FtsH 억제 CII 충분하여

cI 전사촉진 Lysogenic cycle

숙주 한 마리에 적은 bacteriophage 감염 (low MOI)

(숙주많다, 영양분에대한숙주간경쟁많다, 숙주

성장느리다나가서다른숙주찾는것이 유리)

초기 CIII 발현량적음 FtsH에의한 CII 분해

CI 낮음 Cro 우세 Lytic cycle

16.2 How Is Gene Expression Regulated in Prokaryotes?

Prokaryotes conserve energy and resources by making certain proteins only when they are needed. To shut off the supply of an unneeded protein, the cell can:

• Downregulate mRNA transcription

• Hydrolyze mRNA, preventing translation

• Prevent mRNA translation at the ribosome

• Hydrolyze the protein after it is made

• Inhibit the protein’s function

16.2 How Is Gene Expression Regulated in Prokaryotes?

E. coli must adapt quickly to sudden changes in food supply. Glucose or lactose may be present.

Uptake and metabolism of lactose involve three proteins:

• -galactoside permease — a carrier protein that moves lactose into the cell

• -galactosidase — an enzyme that hydrolyses lactose

• -galactoside transacetylase — transfers acetyl groups to certain -galactosides

Figure 16.10 The lac Operon of E. coli

A typical operon consists of:• A promoter• Two or more structural genes• An operator — a short stretch of DNA between

the promoter and the structural genes

16.2 How Is Gene Expression Regulated in Prokaryotes?

Structural genes specify primary protein structure — the amino acid sequence.

The three structural genes for lactose-metabolizing enzymes are adjacent on the chromosome, share a promoter, and are transcribed together.

A gene cluster with a single promoter is an operon — the one that encodes for the lactose-metabolizing enzymes is the lac operon.

Figure 16.11 The lac Operon: An Inducible System

allolactose

Allolactose

* lac operon의 inducer 는 lactose가아니라 allolactose이다

Lactose가없어도 lac operon의유전자는아주소량발현되고있어서-galactoside permease와 -galactosidase가소량존재

Lactose가존재하면 -galactosidepermease에의해 lactose가세포내로들어온후, 일부가 -galactosidase(두가지활성을가지고있고, 주활성은lactose를분해하는것이지만)에의해allolactose로바뀜

Allolactose가 inducer 로작용

Operon으로부터유전자발현

16.2 How Is Gene Expression Regulated in Prokaryotes?

Mechanisms to control operon transcription:

1. An inducible operon regulated by a repressor protein and a inducer lac operon

2. A repressible operon regulated by a repressor protein and a co-repressor trp operon

• Positive regulation of lac operon by an activator protein

Figure 16.12 Catabolite Repression Regulates the lac Operon

16.2 How Is Gene Expression Regulated in Prokaryotes?

An activator protein can increase transcription through positive control.

If high lactose & low glucose, cAMP receptor protein (CRP) binding to the lac operon promoter activates the lac operon.

CRP (= catabolite activator protein, CAP) makes RNA polymerase-promoter binding more efficient, and increases structural gene transcription.

If high glucose, CRP does not bind to the lac operon promoter and efficiency of transcription is reduced.

An example of catabolite repression — a system of gene regulation in which the presence of a preferred energy source represses other catabolic pathways.

16.2 How Is Gene Expression Regulated in Prokaryotes?

The trp operon of E. coli has repressible system — repressed when molecules called co-repressors bind to their repressors.

precursor → → → → → tryptophan

Binding of co-repressor → repressor changes shape and binds to operator → inhibits transcription

16.2 How Is Gene Expression Regulated in Prokaryotes?

Difference in two types of operons:

In inducible systems — If a metabolic substrate or its metabolite (inducer) binds to a repressor, then the repressor is detached from the operator and transcription is allowed.

Generally, inducible systems control catabolic pathways —turned on when substrate is available.

In repressible systems — a metabolic product (co-repressor)binds to a repressor, which then binds to the operator and blocks transcription.

Repressible systems control anabolic pathways —turned on until product concentration becomes excessive; turned off when product is excessive.

Figure 16.9 Two Ways to Regulate a Metabolic Pathway

The rate of a metabolic pathway can be regulated in two ways:- Allosteric regulation of enzyme-catalyzed reactions allows rapid fine-tuning.- Regulation of protein synthesis (regulation of the concentration of enzymes)

is slower but conserves resources.

16.3 How Is Eukaryotic Gene Transcription Regulated?

Eukaryotic gene expression:

Must be regulated to ensure proper timing and location of protein production.

Regulation can occur at multiple points in transcription and translation.

Figure 16.13 Potential Points for the Regulation of Gene Expression

16.3 How Is Eukaryotic Gene Transcription Regulated?

Transcription factors (regulatory proteins) act at eukaryotic promoters — regions of DNA where RNA polymerase binds and initiates transcription.

Two important sequences in a promoter:

• Recognition sequence — recognized by RNA polymerase

• TATA box — where DNA begins to denature and expose the template strand

Transcription factors must assemble on the chromosome before RNA polymerase can bind to the promoter.

TFIID binds to the TATA box; then other transcription factors bind, forming a transcription complex.

Figure 16.14 The Initiation of Transcriptionin Eukaryotes

16.3 How Is Eukaryotic Gene Transcription Regulated?

Some regulatory sequences, such as the TATA box, are common to promoters of many genes; recognized by transcription factors found in all cells.

Other sequences are specific to a few genes and are recognized by transcription factors found only in certain tissues. These play an important role in cell differentiation.

16.3 How Is Eukaryotic Gene Transcription Regulated?

Besides the promoter, other sequences bind regulatory proteins that interact with RNA polymerase and regulate rate of transcription.

Some are positive regulators — enhancers; others are negative — silencers.

The combination of factors present determines the rate of transcription.

Figure 16.15 Transcription Factors, Repressors, and Activators

Figure 16.17 Coordinating Gene Expression

Genes to be regulated simultaneously may be far apart or on different chromosomes.

Gene expression is coordinated if they have the same regulatory sequences that bind same transcription factors.

Example: A regulatory sequence in plant genes called stress response element (SRE) — encodes for proteins needed to cope with drought.

16.4 How Do Epigenetic Changes Regulate Gene Expression?

Epigenetics refers to changes in expression in a gene or set of genes, without a change in the DNA sequence.

Changes are sometimes heritable and stable, but are reversible.

Includes two processes: DNA methylation and chromatin remodeling by chromosomal protein (histone) alterations.

Figure 16.18 DNA Methylation: an Epigenetic Change

Some cytosine residues in DNA are modified by adding a methyl group covalently to the 5-carbon — forms 5-methylcytosine.

DNA methyltransferase catalyzes the reaction in regions rich in CG called CpG islands — usually exist in promoters.

When DNA replicates, a maintenance methylase catalyzes formation of 5-methylcytosine in the new strand.

Methylation pattern may be altered.

Demethylase can catalyze the removal of the methyl group.

16.4 How Do Epigenetic Changes Regulate Gene Expression?

Effects of DNA methylation:

• Methylated DNA attracts proteins that are involved in repression of transcription and can inactivate DNA.

• Important in development — early demethylationallows many genes to become active.

• In cancer, misregulation can occur in oncogenes and tumor suppressors.

16.4 How Do Epigenetic Changes Regulate Gene Expression?

Chromatin remodeling is the alteration of chromatin structure.

Nucleosomes contain DNA and histones in a tight complex, inaccessible to RNA polymerase.

Each histone has a “tail” at its N terminus with positively charged amino acids.

Histone acetyltransferases(HAT) reduce the tail’s charge by adding acetyl groups to the amino acids.

Histone acetylation opens up nucleosomes and activates transcription.

Figure 16.19 Epigenetic Remodeling of Chromatin for Transcription

16.4 How Do Epigenetic Changes Regulate Gene Expression?

Histone deacetylase(HDAC) remodels chromatin by removing the acetyl groups from the histones, repressing transcription.

In some cancers, genes that inhibit cell division are excessively deacetylated.

Drugs acting as histone deacetylaseinhibitors may be useful to treat the cancer, if they can activate those genes.

16.4 How Do Epigenetic Changes Regulate Gene Expression?

Twin studies show that the environment can produce different epigenetic modifications, and thus differences in gene regulation in genetically identical individuals.

Environmental factors that may lead to epigenetic changes:

• Stress — in brain, some genes become heavily methylated.

• Addiction may produce different acetylation patterns.

• Psychosis changes methylation patterns in sperm: heritable?

16.5 How Is Eukaryotic Gene Expression Regulated After Transcription?

Eukaryotic gene expression can be regulated post-transcriptionally in the nucleus before mRNA export, or after mRNA leaves.

Control mechanisms involve alternative splicing of pre-mRNA, microRNAs, repressors of translation, or regulation of protein breakdown.

Figure 16.22 Alternative Splicing Results in Different Mature mRNAs and Proteins

Figure 16.23 mRNA Inhibition by MicroRNAs

MicroRNAs(miRNAs) —small molecules of noncoding RNA — are important regulators of gene expression.

Each miRNA is about 22 bases long and has many targets.

Proteins guide miRNA to target mRNA —translation is inhibited and mRNA is degraded.

“RNA interference(RNAi; RNA 간섭)”

16.5 How Is Eukaryotic Gene Expression Regulated After Transcription?

Protein and mRNA concentrations are not consistently related — governed by factors acting after mRNA is made.

Cells either block mRNA translation or alter how long new proteins persist in the cell.

Three ways to regulate mRNA translation:

• miRNAs can inhibit translation.

• GTP cap on 5′ end of mRNA can be modified — if cap is unmodified, mRNA is not translated.

• Repressor proteins can block translation directly.

Figure 16.24 A Proteasome Breaks Down Proteins

Protein longevity is regulated — protein content is a function of synthesis and degradation.

Ubiquitin attaches to a protein to be destroyed and attracts other ubiquitins.

This complex binds to a proteasome — a large complex where the ubiquitin is removed and the protein is digested.