Griffiths Wessler Carroll Doebley

Introduction to
Genetic Analysis
TENTH EDITION

CHAPTER 11

Regulation of Gene Expression in

Bacteria and Their Viruses
2012 W. H. Freeman and Company

CHAPTER OUTLINE
11.1
11.2
11.3
11.4
11.5

Gene regulation
Discovery of the lac system: negative control
Catabolite repression of the lac operon: positive control
Dual positive and negative control: the arabinose operon
Metabolic pathways and additional levels of regulation:
attenuation
11.6 Bacteriophage life cycles: more regulators, complex
operons
11.7 Alternative sigma factors regulate large sets of genes

Gene Regulation

Gene Regulation

Differential gene expression is important!

Not every gene is expressed all the time
Cells have mechanisms that:
Recognize environmental conditionswhen they
should active or repress transcription of genes
Turn on or off (like a toggle switch) transcription of
each gene or groups of genes

Types of Gene Expression

Genes can be characterized by their expression

Some genes are on all the time these are

constitutive genes
Include housekeeping genes
Encode proteins that need to be transcribed continually
Ex. Actin or ubiquitin

Some genes are transcribed only when needed

these are facultative genes
Turned on/off in response to change in the cells
environment (e.g. available nutrients)
Or dependent on the cell cycle

Types of Gene Expression

Regulation of facultative genes think of services

Constitutive genes
On all the time
Ex: Utilities like BC Hydro

Two main kinds of facultative genes

Inducible genes
Gene is normally off switched on when needed
Ex: RCMP or Fire Department

Repressible genes
Gene is normally on switched off when necessary
Ex: Canada Post

Types of Gene Expression

Control of transcription

Two main ways to control transcription of specific

genes
Depends on regulatory proteins
Positive control activator protein increases
transcription of gene (activator binding site)
Negative control repressor protein decreases
transcription of gene (bind to operator)

Regulatory proteins bind DNA near gene

Require specific DNA nucleotide sequences
Regulatory proteins are very specific

Regulatory proteins control transcription

Positive: presence of activator

allows transcription of gene

Negative: absence of repressor

allows transcription of gene

Regulatory proteins control transcription

Regulatory proteins are also regulated!

Effector molecules can regulate activators

and repressors
Often small molecules
May be metabolites

Activate or deactivate regulatory proteins

Allosteric regulation is common
Effector binds to regulatory protein
Changes conformation of DNA binding site of regulatory
protein
Changes its ability to bind DNA

Allosteric effectors bind to regulatory proteins

Repressor protein controls the lac operon

The Lac Operon (a set of genes) in E. coli to metabolize

lactose a disaccharide

Metabolism of lactose requires two proteins

Lac permease (lacY) transports lactose into cell
-Galactosidase (lacZ) cleaves lactose into
glucose and galactose (monosaccharides)

Genes are transcribed onto a single mRNA

Prokaryotes can make mRNA with multiple genes
Lack of introns/exons and mRNA processing makes this
possible
Called polycistronic mRNA

Repressor protein controls the lac operon

The Lac Operon (a set of genes) in E. coli to metabolize

lactose a disaccharide

Genes are transcribed onto a single mRNA

Jacob & Monod discovered three genes by
classical genetic approach
Used mutant strains of E. coli
We will revisit their experiments later in the
semester

Repressor protein controls the lac operon

The Lac Operon (a set of genes) in E. coli to metabolize

lactose a disaccharide

The Lac operon is inducible

Turned on when needed

The Lac operon in under negative control

Controlled by a repressor (lacI)
Repressor is deactivated by an effector molecule
(inducer)
Lactose acts as the inducer

Repressor protein controls the lac operon

Lactose is broken down into two sugars

The lac operon is transcribed only in the presence of lactose

The lac operon is transcribed only in the presence of lactose

The lac operon is transcribed only in the presence of lactose

Lac operon regulation lactose induces expression

The lac repressor is encoded by lacI

lacI is located some distance from the lac operon

The repressor binds the lac operator (O)

between the promoter and the lacZ gene
Lactose is an allosteric effector of the lac
repressor
If lactose is present it binds the repressor
The repressor changes shape and falls off the DNA
RNA polymerase can bind the lac promoter

The lac operon

Experiments using the lac operon

Lactose is an inducer of the lac operon

However, it is broken down by -Galactosidase
Difficult for experimentation!

Other (lactose-shaped) molecules may induce

the lac operon
Isopropyl--D-thiogalactoside (IPTG) can bind to
the lac repressor molecule, inactivating it
-Galactosidase does not act on IPTG
Switches on the lac operon, but is not used up

Structure of IPTG

Regulation of the lac operon

What if lactose and glucose are present?

E. coli prefers glucose over lactose
If both are present lac operon is kept
off
A positive control mechanism is at work
Catabolite repression a breakdown
product of metabolism controls
transcription
If glucose is present, ATP is plentiful
If glucose is absent, AMP levels
increase
One version of AMP is cyclic AMP
(cAMP)

Glucose levels control the lac operon

Regulation of the lac operon

The catabolite cAMP controls transcription

cAMP binds catabolite activator protein

(CAP) cAMP-CAP complex
cAMP-CAP complex binds lac promoter
Acts as activator and increases transcription

Added level of control ensures proper

transcription:
ON: high lactose and low glucose
OFF: the rest of the time

Glucose levels control the lac operon

Many DNA binding sites are symmetrical

Symmetrical binding sites make control easier!

Binding of CAP bends DNA

Negative and positive control of the lac operon

Negative and positive control of the lac operon

Negative and positive control of the lac operon

Negative and Positive Control of Transcription

Cells have different ways to regulate transcription

Repression and activation compared

(Generic)

Repression and activation compared

(Generic)

Dual Positive and Negative Control

Other control systems use combinations of repression

and activation

Arabinose Operon in E. coli

Arabinose is a sugar
araB, araA, araD genes (polycistronic mRNA)
Encode proteins to break down sugar

araI is the initiator region

Map of the ara operon

The ara operon contains several genes:

Structural genes encode proteins

Regulation of the ara Operon

AraC protein controls the ara operon

The gene araC encodes a regulatory protein

AraC
AraC is both an activator and a repressor

araI is the initiator region of the operon

It affects binding of RNA pol to the promoter

Arabinose is an effector molecule

Arabinose + AraC protein bind araI

CAP + cAMP also bind araI

(CAP + cAMP) + (Arabinose + AraC) = lots of RNA

AraC serves as an activator and as a repressor

Arabinose operon is switched on by:

AraC + Arabinose (= lots of arabinose)
CAP + cAMP (= low levels of glucose)
What if there is no arabinose in the cell?

AraC serves as an activator and as a repressor

Gene order in the trp operon corresponds to reaction order in the biosynthetic pathway

The trp operon encodes genes to synthesize tryptophan

Regulation of the trp operon

trp operon controls synthesis of tryptophan

trp gene expression is dependent on the

levels of tryptophan (trp) in the cell
trp operon is under control of a repressor
Encoded by the gene trpR
The trp repressor is activated by tryptophan
Stops expression of the trp operon by binding to
the operator trpO

Regulation of the trp operon

trp operon controls synthesis of tryptophan

The trp operon is also regulated by

attenuation
Attenuation means turning downnot all the
way off

This mechanism is built into the trp mRNA

The trp mRNA leader sequence contains an attenuator region and two tryptophan codons

Two trp codons (UGG) in a

row upstream from trp operon

Abundant tryptophan attenuates transcription of the trp operon

Regulation of the trp operon

Attenuation fine-tunes gene expression

Attenuation affects translation not transcription

The trp operon is an example of how regulatory
mechanisms allow fine regulation of gene
expression
Critical for maintaining homeostasis
Allows quick adjustments to respond to changes in
the environment

Tryptophan is not the only system with

attenuation of gene expression

Leader peptides of amino acid biosynthesis operons

Regulation of gene expression

Phage gene regulation

Bacteriophage life cycles: more regulators,

complex operons

Image: www.zyvexlabs.com

Helix-turn-helix is a common DNA-binding motif

DNA binding depends on physical structures

Amino acid side chains determine the specificity of DNA binding