Chapter 13. Regulation of gene expression References: 1.Stryer: “Biochemistry”, 5 th Ed. 2.Hames & Hooper: “Instant Notes in Biochemistry”, 2 nd Ed.

Chapter 13. Regulation of gene expression

References: 1. Stryer: “Biochemistry”, 5th Ed.2. Hames & Hooper: “Instant Notes

in Biochemistry”, 2nd Ed.

1. Basic principles of gene control

What is gene expression?

It is a process by which a gene's information is converted into the structures and functions of a cell.

For a protein encoding gene, it is a process of the transcription of a gene into mRNA, and the latter is translated into protein.

How to control gene expression?

In prokaryotic cells, gene expression is regulated primarily at the level of transcription by metabolites;

In eukaryotes it is controlled by much more complex mechanisms, including the action of protein factors, hormones, etc.

Control of gene expression in prokaryotes

R Structural gene

SubstrateProduct

Enzyme

mRNA

DNA

R

Control of gene expression in eukaryotes

DNA

Protein

mRNARNA

synthesis

InactivemRNA

mRNA

InactiveProtein

Transcript.control

1

RNA processingcontrol

2

RNAtransportcontrol

3

mRNA degradation

control

5

Translationcontrol

4

Protein activitycontrol6

Nucleus

Cytosol

2. Regulation of Prokaryotic gene expression– the operon theory

Operons are groups of genes that function to produce proteins needed by the cell.

There are two types of genes in operonsA. Structural genes code for proteins

needed for the normal operation of the cell.

B. Regulator genes code for proteins that regulate other genes.

lac I lac Z lac A lac Y PlacI Plac Olac

Plac : promoter; Olac: operator; lac Z: -galactosidase; lacY: permease; Lac A: transacetylase; lac I: structural gene for lac repressor; PlacI : promoter for lac I.

Lactose Operon

Regulation of the lac operon in E. coli.

p i p o z y a

The lact Operon

RepressormRNA

Repressor

The repressor binds to the operator region and prevents RNA polymerase from transcribing the structural genes

In the presence of lactose

p i p o z y a

The lact Operon

Lactose binds the repressor and allows RNA polymerase access to the operator, resulting in transcription of the structural gene

-galactosidase permease transacetylase

RepressormRNA

Repressor

Lactose

mRNA

In the presence of glucose & lactose

p i p o z y a

The lact Operon

glucose

AdenylcyclasecAMP ATP

L actose

Low level of transcription

In the absence of glucose and presence of lactose

p i p o z y a

The lact Operon

L actose

High level of transcription

AdenylcyclasecAMP ATP

CAP

active

CAP: catabolite activator protein

Tryptophan Operon

The trp operon encodes the genes for the synthesis of tryptophan

L A BP,O a CDE

Genes for enzymes

P: promoter, O: operator, a: attenuator, L: leader sequence, A,B,C,D,E: enzymes

of the Trp pathway

Regulation of the trp operon in E. coli.

Binding of Trp to the trp repressor increases the activity of the repressor, and therefore Trp is known as a co-repressor.

Expression of the trp operon is also regulated by attenuation. The attenuator region contains tandem Trp codons, which play a role to attenuate the transcription of the following genes.

Regulation of the trp operon

Regulation of trp operon by attenuation

1) The regulation of eukaryotic gene expression differs from that of prokaryotes in:

A) Eukaryotic RNA polymerases cannot transcribe DNA on their own—a multisubunit transcriptional apparatus must assemble first at the TATA box of the gene.

3. Regulation of eukaryotic gene expression.

B) Activators and repressors of eukaryotic gene expression act by altering the rate of formation of the transcriptional complex, while those of prokaryotes act by binding to the promoter or operator.

C) Eukaryotic genes are controlled by multiple proteins rather than by just one or two.

2) Zinc fingers regulate eukaryotic gene expression by binding to DNA strands

C

HC

H

HC

HCZ n Z n

Z in c f in g e r L in k e r Z in c f in g e r Zinc finger Linker Zinc finger

For example, TFIIIA is a transcriptional factor for transcription of the 5S genes by RNA polymerase III. It contains nine Zinc fingers. The Zinc fingers bind to DNA in the major groove to form the initiation complex.

C

HC

H

HC

HCZn Zn

DNA

Steroid hormones (e.g. cortisol, testosterone, progesterone) play their roles by forming hormone-receptor complexes, which then bind to specific sites on DNA, and induce or repress the transcription of the particular gene.

3) Regulation of eukaryotic gene expression by hormones

Steroid hormone

DNA

mRNA

mRNAproteineffects

receptor

They are eukaryotic transcriptional regulators, which form dimers to bind DNA strands around the major groove.

Leucine zipper proteins mediate the effect of cAMP on transcription by binding to the cAMP response element (CRE).

4) Leucine zipper proteins:

CRE structure is a palindromic 8-bp DNA sequence:

5’-TGACGTCA-3’

3’-ACTGCAGT-5’

5’-TGACGTCA-3’

3’-ACTGCAGT-5’

CRE binding protein

DNA binding of leucine zipper protein

Leucine zipper protein

DNA helix

For example, cAMP response element binding protein (CREB) has the leucine zipper region:

cAMP protein kinase A (PKA) phosphorylation of CREB dimerization of CREB binding of CREB to DNA activation of transcription of the gene.

Signaling through cAMP & PKA to CREB

PP

Phosphorylation

Dissociation Nuclear translocation

Target gene activation

Cytoplasm

Nucleus

AC

cAMP

C

C

C

C

CBP

P

PKA

CREB

Dimerization of a zipper protein increases its efficacy as a transcriptional activator.

CREB is a target for the Ca2+-calmodulin-activated CaM kinase II, protein kinase C, and other kinase, which suggests that it integrates many signals for DNA transcription.

CREB as a target for other signal pathways