Regulation of Gene

Expression

Ricardo R. Santos, MD
 Learning Objectives

1. Discuss the principles of gene regulation

2. Explain the operon system which is the

regulation of gene expression in bacteria

3. Describe the regulation of eukaryotic

gene expression

4. Discuss other modes of regulation -

gene amplification, gene rearrangement,
modification of bases, etc.
Principles of Gene Regulation

Of the 4,000 or so genes in the bacterial

genome or 29,000 genes in the human
genome, only a fraction are expressed at
any given time (Leninger Principles of
Biochemistry, 5th Ed.)

1. Differential expression of genes

a) some gene products are present in
very large amount, e.g. elongation
factors for protein synthesis

b) other gene products are produced in

much smaller amounts, e.g. enzymes
that repair rare DNA lesions
2. Regulated expression of genes is
required for

a) Adaptation – the need for enzymes and

hormones in certain metabolic pathways
may wax or wane as food sources
change

b) Development – during development of a

multicellular organism, some proteins
that influence cellular differentation are
present for just a brief period of time
3. Specialization of cellular function, e.g.
high concentration of hemoglobin
in erythrocytes

Two Types of Gene Regulation

1. Positive regulation – increased expression

of genetic information; activator (positive
effector or modulator) mediates positive
regulation

- double negative has the effect of acting as

a positive, e.g. an effector that inhibits a
negative modulator brings about a positive
regulation (derepressed)
2. Negative regulation – expression of genetic
information is decreased by the presence of
a repressor (negative regulator)

Three types of responses to a regulatory

signal

1. Type A response – increased gene

expression that is dependent upon the
continued presence of the inducing signal
(inducer) such as hormones, nutrients or
growth factors
2. Type B response - increased gene
expression that is transient even in the
continued presence of the regulatory
signal.
Example: response-desensitization
recovery effects of many pharmacologic
agents.

3. Type C response - an increased extent of

gene expression that persists indefinitely
even after removal of the regulatory signal.
This occurs during development and
differention of functions of a tissue or organ.
Alteration of gene expression involves
modulation of

1. Gene transcription – most common

2. Gene amplification
3. Gene rearrangement
4. Posttranscriptional modifications
5. RNA stabilization
6. Translational control
7. Posttranslational modifications
8. Protein stabilization
Regulation of Gene Expression in Bacteria

Operon - a linear array of genes involved in a

metabolic pathway, e.g. lac operon and
trp operon.
- can be regulated by a single promoter region

Cistron – smallest unit of genetic expression;

codes for a subunit of a protein
(one cistron, one subunit concept)

Polycistronic mRNA - a single mRNA that

encodes more than one separately
translated protein
Inducible gene - one whose expression
increases in response to an inducer or
activator.
-has low basal rate of transcription

Constitutive gene - one which is expressed at

a constant rate and not subject to regulation.
-referred to as housekeeping gene

Some inducible gene that undergo mutation

become constitutively expressed. This is called
constitutive mutation.
 The Lac Operon

- Described by Francois Jacob and Jacques

Monod in 1961

- They explained bacterial gene expression by

studying lactose metabolism in E. coli

- Lac operon describes how two adjacent genes

involved in lactose metabolism were
coordinately regulated by a genetic element
located at one end of the gene cluster
These genes are

1. lac Z gene – structural gene for β-galactosidase

which hydrolyzes lactose to galactose and
glucose

2. lac Y gene – structural gene for permease

which transports lactose into the cell

3. lac A gene – encodes a thiogalactoside

transacetylase which modify toxic
galactoside to facilitate their removal from
the cell
Other components of the lac operon

1. lac promoter & lac operator – regulatory

region

2. lac I – encodes the repressor protein Lac I

Note: - Lactose is the inducer

- When lactose and glucose are present,
the cell metabolizes first glucose
 How does the lac operon works?

A. Without lactose or with lactose and

glucose

1. lac I gene is constitutively expressed to form

4 repressor subunits that binds at the
operator locus thus preventing the
transcription of lac Z, Y and A genes by
RNA polymerase

lac I repressor is a negative regulator

B. With lactose and no glucose

1. Lactose molecules bind to repressor subunits

thereby inactivating the repressors

2. Repressors cannot bind to the operator site.

3. In the presence of cAMP and its binding

protein (CAP, catabolite gene activator
protein, cAMP regulatory protein [CRP] )
RNA polymerase can now transcribe the
structural genes Z, Y and A into their
corresponding enzymes.
Regulation of Eukaryotic Gene Transcription

A. Differential expression of genes

e.g. B-globin gene cluster is in “active”
chromatin in the reticulocyte but in
“inactive” chromatin in muscle
cells
B. Chromatin remodeling
e.g. Histone acetylation by acetylase
 Acetylation of lysine residues in
amino terminal tails
 Reduced positive charge of these
tails
  Decreased binding affinity of
histone to DNA
 Disruption of nucleosomal
structure
 Regulatory DNA elements become
more accessible to transcription
factors
C. Presence of enhancer and repressor
elements
– Enhancer binding proteins acting as
transcription activators facilitate binding of
the basal transcription machinery to the
promoter.
D. Regulatory proteins having special motifs
bind with high affinity to the correct region of
the DNA
– Three unique motifs
1) Helix-turn-helix
2) Zinc finger
3) Leucine zipper

 Motifs enhance binding of the protein

to DNA
 Protein provides a ligand-binding site
for modulators or effectors
E. Other modes of regulation to DNA
– Gene amplification
– Gene rearrangement
– Transposition
– Methylation of CG-rich regions
– (CpG islands)
 Gene Amplification
- Increase in the number of genes available for
transcription  increase in the number of
RNA and proteins

- Generated by a process of repeated initiations

during DNA synthesis thereby providing
multiple sites for gene transcription

- Basis of development of drug resistance, eg, to

methotrexate, by increasing the number of
dihydrofolate reductase.
 Gene Rearrangement

- Process involved in the synthesis of different

antibodies by lymphocytes

- Allows the generation of 109 - 1011 different

immunoglobulins from a single gene
-The variable region is the result of somatic
recombination of segments within both
the light - and the heavy-chain genes
 Transposons (Tn, Jumping DNA)

- Mobile segments of DNA that move in a random

manner from one site to another on the same
or different chromosome

- Mediated by transposase, enzyme that cuts out

and inserts the Tn at a new site and is copied

- Replicative transposons may involve an RNA

intermediate and is called retrotransposon

- May cause diseases such as hemophilia A &

Duchenne muscular dystrophy
 Transposons (Tn, Jumping DNA)

- May cause diseases such as hemophilia A &

Duchenne muscular dystrophy

- Exchange of plasmids that contain transposon

carrying antibiotic resistance genes among
bacterial cells may confer antibiotic resistance
to the recipient bacteria.
 Methylation of CG-rich regions

- Promoter region of the gene contains CpG

islands (CG-rich region)

- Transcriptionally active genes are less

methylated

- This suggests that DNA hypermethylation

silences gene expression

- Methylation is catalyzed by methyltransferases

using S-adenosylmethionine (SAM) as the
active methyl group donor