Gene regulation

Thanet Sophonnithiprasert
Biochemistry Unit
Department of Medical Sciences
Faculty of Sciences
Rangsit University

For BCH 100 203 inter student

Gene regulation
refers to the processes that cells use to turn the information on
genes into gene products DNAto Protein
change
Gene regulation
Gene regulation in prokaryotic cells are differ from eukaryotic cells

Nucleus membrane and chromatin structure are critical point

Gene regulation
Level of regulation in bacterial gene expression

Bacteria might regulate gene expression by controlling transcription,

controlling translation, or controlling protein function post-translationally
Why the regulation of gene expressions
are necessary ?
Absolutely essential for:
The cell growth
The cell development
The cell differentiation

Normally, gene regulation is responded to

environment and keep existence of living
iTuneswig as
Type of gene expression
Separated by frequency of gene expression and effect of metabolite:

Gene

unregulated regulated
Constitutive gene
Active at all times and inducible repressible
constantly expressed Normally turned off Normally turned on
Example: ribosomal
Catabolic pathways Anabolic pathways
protein, RNA polymerase
Metabolite acts as Metabolite acts as
, glycolysis enzyme etc.
inducer repressor in feedback
inhibition
Gene expression in prokaryote

Most prokaryotic gene are regulated in units

called “Operon system”, first described by
Jacob & Monod (1961)

Operon model
Operon model
Consist of:
Regulator gene: operon regulation
Operon: include promoter, operator and structural genes
Operon model
Regulator gene:
Produces a repressor protein, which is allosteric regulatory protein, that
inhibits an operator region when combined with it
One of constitutive gene (unregulated gene)
Operon model
Promoter:
This region’s position is always before an operator region
Region on DNA where RNA polymerase binds to start transcription
Acts as the on/off switch for gene
Operon model
Operator:
This region’s position is always before structural genes
Specific binding for repressor which expressed from regulator gene
Region on DNA that controls access of RNA polymerase to the genes
Operon model
Structural genes:
Genes to be transcribed by RNA polymerase
Divided to:
monocistronic: 1 gene per structural gene
polycistronic: more than 1 genes per structural genes
Operon model
Structural genes:
Genes to be transcribed by RNA polymerase
Divided to:

Monocistronic:
Structural gene
promoter operator terminator start codon
5 Gene A 3
RBS

stop codon

Polycistronic:
Structural gene

promoter operator terminator

5 Gene A Gene B Gene C 3
RBS

RBS

RBS
Inducible operon
Regulator gene of inducible operon express the active repressor for
regulate this operon
The metabolites act as inducer for activate gene switch on
The lac operon is a common example of an inducible operon for study
Regulator gene lac operon

genes in structural gene is contain:

- lac Z gene encodes b-galactosidase,
an intracellular enzyme that cleaves the disaccharide lactose into glucose and galactose
- lac Y gene encodes b-galactoside permease,
a membrane-bound transport protein that pumps lactose into the cell
- lac A gene encodes b-galactoside transacetylase,
an enzyme that transfers an acetyl group from acetyl-CoA to β-galactosides.
Regulation of lac operon
No inducer (no lactose available)
The regulator gene is synthesize the free repressor
protein in active form

repressor protein bind to the operator region,

cause the promoter region is not free

RNA polymerase cannot bind to

the promoter region

Cannot begin the transcription

Regulation of lac operon
No inducer (no lactose available)
Regulation of lac operon
Add inducer (lactose available)
The regulator gene is synthesize the free repressor
protein in active form

inducer bind to repressor protein,

cause repressor become to inactive form

inactive repressor cannot bind to the operator gene,

cause RNA polymerase can bind to promoter gene

the transcription start

Regulation of lac operon
Add inducer (lactose available)
Dual regulation of lac operon
Glucose repression:
How does E. coli respond
to lactose?

The presence of lactose

without glucose stimulates
expression of that gene

It is "cheaper" to grow on
glucose than on lactose, so
bacteria will not metabolize
lactose in the presence of
abundant glucose
Dual regulation of lac operon
Glucose repression:
Glucose regulates cAMP levels

cAMP bind to CRP protein

become CRP-cAMPs, activity
like transcription factor

CRP-cAMP activates
transcription of other genes
Dual regulation of lac operon
Glucose repression:
cAMP-CRP bind to CAP site (or Activator
binding site) and facilitates the binding of RNA
polymerase and greatly increases lac operon
transcription when repressor is not bound
Dual regulation of lac operon
Glucose repression:
Dual regulation of lac operon
Summary:
Repressible operon
A gene system is repressible if excess quantities of (usually) the end product
of the pathway (as repressor) leads to cessation of transcription of the
genes encoding the enzymes of the (anabolic) pathway
Metabolite interact with aporepressors and activate them, pause of
transcription of the genes encoding the enzymes
The trp operon is a common example of an repressible operon for study
Regulator gene trp operon

Chorismate Tryptophan
 Regulation of trp operon
Anabolic metabolite (tryptophan molecules) is low concentration
The regulator gene is synthesize the free aporepressor
protein in inactive form

aporepressor protein cannot bind to the operator gene,

cause the promoter gene is free

RNA polymerase can bind to

the promoter gene

begin the transcription

 Regulation of trp operon
Anabolic metabolite (tryptophan molecules) is low concentration

Repressor remain inactive, operon on

more animation… Click here!

 Regulation of trp operon
Anabolic metabolite (tryptophan molecules) is high concentration
The regulator gene is synthesize the free aporepressor
protein in inactive form

tryptophan bind to aporepressor protein,

cause aporepressor become to active form

active repressor can bind to the operator gene,

cause RNA polymerase cannot bind to promoter gene

pause the transcription

 Regulation of trp operon
Anabolic metabolite (tryptophan molecules) is high concentration

Repressor activated, operon off

more animation… Click here!
Dual regulation of trp operon
Attenuator site regulation:
How cells control level of tryptophan immediately?
Because tryptophan is not synthesized by structural genes of trp operon directly
Translational control facilitate to regulation of trp operon (mRNA level)

4 domains
 Dual regulation of trp operon
Attenuator site regulation:

I
L

St
→

ProjetIter
←
I
y
Dual regulation of trp operon
Attenuator site regulation:

1- .

Trp
Trp Trp
Gene regulation in prokaryote
Prokaryotic cells regulate gene expression by two mechanisms:

Gene

unregulated regulated

inducible
lac operon: lactose/IPTG induction
Dual regulation with glucose repression
Common use in regulation of gene
expression in genetically modified bacteria
repressible
trp operon: tryptophan repression
Dual regulation with trpL gene
Common use in explanation of
feedback regulation
Gene regulation in eukaryote
No “Operon” in eukaryote
Six Steps at which eukaryotic gene expression are controlled
Eukaryotic gene regulation is more complex because eukaryotes possess a
nucleus (transcription and translation are not coupled)
Transcriptional control
Regulation of transcription controls when transcription occurs and how
much RNA is created
Transcription of a gene by RNA polymerase can be regulated by many
mechanisms, such as:
Transcription preinitiation complex
Chromatin remodeling control
DNA methylation
Transcription Preinitiation complex

The preinitiation complex helps position RNA polymerase II over gene

transcription start sites, denatures the DNA, and positions the DNA in the
RNA polymerase II active site for transcription

This regulatory proteins:

(trans)-activators
co-activators
basal transcription factors

Response elements are short sequences of DNA within a gene promoter region that
are able to bind specific transcription factors and regulate transcription of genes
Activators bind to enhancers
Repressors bind to silencers

Animation… Click here!

Chromatin remodeling control

Heterochromatin
Euchromatin
Chromatin remodeling control
Suppress transcription
increase chromatin
condensation
“Histone deacetylase (HDAC)”

Enhance transcription
decrease chromatin
condensation
“Histone acetyl transferase (HAT)”
Chromatin remodeling control
DNA methylation
Transcriptionally active genes possess significantly lower levels of methylated
DNA than inactive genes,.
5 -methylation of cytosine of CpG sequences is common in eukaryotic DNA, active
genes tend to be undermethylated.
DNA methylation
Transcriptionally active genes possess significantly lower levels of methylated
DNA than inactive genes,.
5 -methylation of cytosine of CpG sequences is common in eukaryotic DNA, active
genes tend to be undermethylated.
Methylation results in a human disease called fragile X syndrome; FMR-1 gene is
silenced by methylation
RNA processing control
Alternative splicing
is a regulated process during gene expression that results in
a single gene coding for multiple proteins

RNA editing
is a molecular process through which some cells can make
discrete changes to specific nucleotide sequences within a RNA
molecule after it has been generated by RNA polymerase
RNA processing control
Alternative splicing
RNA processing control
RNA editing
RNA transport control
Eukaryote mRNA transport is regulated
Some experiments show ~1/2 of primary transcripts never leave the
nucleus and are degraded
Mature mRNAs exit through the nuclear pores
Ribonucleoprotien (RNP) contain mature mRNA and transport out nucleus
to cytoplasm
Translational control
Unfertilized eggs are an example, in which mRNAs (stored in the egg/no
new mRNA synthesis) show increased translation after fertilization)

Eukaryotic Initiation Factor 2 (eIF2) is a eukaryotic initiation factor. It is

required in the initiation of translation. eIF2 mediates the binding of
tRNAmet to the ribosome in a GTP-dependent manner. eIF2 is a
heterotrimer consisting of an alpha (also called subunit 1), a beta (subunit
2), and a gamma (subunit 3) subunit
Translational control
Regulation of eIF2a by heme (in heme-regulated inhibitor kinase)
RNA degradation control
All RNAs in the cytoplasm are subject to degradation
tRNAs and rRNAs usually are very stable; mRNAs vary considerably
Stability may change in response to regulatory signals and is thought to be a major
regulatory control point
Protein activity control
Protein builded after translation can be:
- Functional
- Have to undergo a maturation process (exo/endopeptidation)
- functional group addition by phosphorylation, acetylation, methylation or other
functional group to functional
Protein activity control
Proteins can be short-lived (e.g., steroid receptors) or long-lived (e.g., lens
proteins in your eyes)
Protein degradation in eukaryotes requires a protein co-factor called
“Ubiquitin”. Ubiquitin binds to proteins and identifies them for
degradation by proteolytic enzymes
Amino acid at the N-terminus is correlated with protein stability and
determines rate of ubiquitin binding
Arg, Lys, Phe, Leu, Trp 1/2 life ≤3 minutes
Cys, Ala, Ser, Thr, Gly, Val, Pro, Met 1/2 life ≥ 20 hours

PEST sequence:
certain proteins with Pro, Gln, Ser, Thr sequence are rapidly degraded
Ubiquitination control
 Summary: step of gene
regulation in eukaryote cell