Gene Expression Systems

Gene Expression Systems in Prokaryotes and Eukaryotes
Expression studies:
1. Analyzing Transcription - Northern blot
- Micro array
- real-time PCR
- Primer extension
2. In vivo Expresion studies
Use of report genes to study regulatory elements
3. Analyzing Translation
- Western blot - immuno assays
- 2D electrophoresis
- proteomics

Studying Transcription
Microarray technique – DNA chips

Studying Transcription
Primer Extension

Promoter Studies
Used reporter genes:
Lac Z
GFP
Luciferase
Promoter

Promoter studies by using reporter genes

Luciferase (luc) systems
firefly species Photinus pyralis
oxidation of compounds called luciferans
( ATP-dependent process)
luciferans emit fluorescense
Expressed luciferase catalyses
mouse with a strain of salmonella
Mice are injected
with LUC+ salmonellas.
Sensitive digital cameras
allow non-invasive detection.
For GT vectors
pics look the same
luminometer measurement

Green fluorescent protein (GFP)
autofluorescent protein from Pacific Northwest jellyfish
Aequorea victoria
ultraviolet light causes GFP
to autofluoresce
In a bright green color
Jellyfish do nothing with UV,
The activate GFP by aequorin
(Ca++ activated,
biolumuniscent helper)

GFP expression is harmless
for cells and animals
GFP transgenic mice from
Osaka University
(Masaru Okabe)
GFP construct could be used for construct tracking in living organism
GFP labelled image of a human tumor.
Vessel on the tumor surface
are visible in black

Engineered proteins
are covering
all the spectrum
San Diego beach scene
drawn with living bacteria
expressing 8 different colors
of fluorescent proteins.
Many more fluorescent proteins are engineered

Use of green fluorescent protein (GFP) as a reporter gene.
Page 119

Analyzing Translation – Western Blot

2 D Electrophoresis

Gene Expression
Transcriptional start
Translational start

Gene Expression
Gene copy number:
1. Plasmid copy number:
The copy-number of a plasmid in the cell is determined by regulating the initiation of plasmid replication.
The initiation of plasmid replication may be controlled by:
the amount of available primer (RNA)
the amount of essential replication proteins
the function of essential replication proteins.
2. Gene dosage -> number of genes integrated into chromosome
- prokaryotic systems -> i.e. Transposons, phages, recombinantion
- mainly eukaryotic systems

Incompatibility of plasmids:
Not all plasmids are able to coexist in the same cell.
Plasmids which have the same replication control functions are incompatible, and are assigned to the same incompatibility group (inc group).
Plasmids of one incompatibility group are related to each other, but cannot survive together in the same bacterial cell, as only different kinds of plasmids are compatible.
Ensures that we can make libraries -> just one plasmid taken up by one cell

Homologous integration into chromosome
Insertion on Bacillus subtilis chromosome

Protein expression in prokaryotic systems
www.qiagen.com
So, this new story
would be about vectors again.
Bacterial expression vectors
have some distinct features:
Inducible promoter systems;
Protein fusions including fused tags;

General advices for one who wants
to produce gene expression
in prokaryotes
1. Do not forget to cut out the intron
2. Check orientation of insert
3. Do fusions with something In-frame
Most obvious and common mistakes:
4. No Post-translation modification
= no product activity

www.wzw.tum.dewww.wzw.tum.de/gene-quantification/ www.wzw.tum.de/gene-quantification/ mrna.html
Introns
Not an issue
when you clone a cDNA

Orientation of insert
(could go backward, if cloned with same-type sticky ends) – use incompatible sticky ends
www.bch.bris.ac.ukwww.bch.bris.ac.uk/staff/ www.bch.bris.ac.uk/staff/ pfdgwww.bch.bris.ac.uk/staff/ pfdg/
teaching/teaching/genes.htm

Fusion proteins.
When expressing
a fusion proteins,
ensure that
both of them are
in the same reading frame
www.bch.bris.ac.ukwww.bch.bris.ac.uk/staff/ www.bch.bris.ac.uk/staff/ pfdgwww.bch.bris.ac.uk/staff/ pfdg/
teaching/teaching/genes.htm

PostTranslational modification
Eukaryotic cells have Golgi system
Prokaryotic cells do not have it
nucleus
Golgi

Efficiency of expression in E.coli
Dependent of:
1. Type of transcription promoter and terminator
2. Affinity of mRNA and prokaryotic ribosome
3. Amount of copies of transgene and its localization
(chromosome or plasmid)
4. Cellular localisation of the protein end-product
5. Efficiency of translation in the host organism
6. Stability of protein product in the host organism
Systems could be optimized on gene to gene basis.
No universal strategy possible

Factors affecting transcription
Promoters (including regulated ones)
PROKARYOTIC!!!!
2. Terminators
PROKARYOTIC!!!!

Variations between prokaryotic promoters are minimal
http://www.blc.arizona.edu/marty/
411

Factors affecting translation
1. Ribosome binding site (RBS)
2. Codon bias
3. Stability of the transcript

Ribosome binding site (RBS) =
translation initiation site
complimentary to 16S rRNA
<10 nt
Avoid hairpins
on 5’ end of gene
(minimize GC content)
Examining the second codon;
better AAA – lysin (13.9% of all E.coli genes).
Expression can vary 15 times.

Codon Usage in E. coli & humans

Codon Optimization Strategies
Chemically synthesize new gene
Alter sequence of the gene of interest to match donor codons to the codons
most frequently used in host organism
Express in different host
choose host with better matching codon usage
Use an engineered host cell
that overexpresses low abundance tRNAs

Commercial E. coli strains
encode for a number of the rare codon genes

Mitochondria and chloroplast genes
Alterations in the Standard Genetic Code in Mitochondria

Factors affecting protein stability
Overall level of protease activity
in bacterial cells
2. N-terminal amino acid affects protein half-life
3. Internal regions containing clusters of certain amino acids
can increase proteolysis
P proline
E glutamic acid
S serine
T threonine
…. Mutate PEST aminoacids….

Protease-deficient host strains
BL21, the work horse of E. coli expression,
is deficient in two proteases
encoded by the lon (cytoplasmic)
and ompT (periplasmic) genes.
It is dangerous
to kill proteases,
it makes E.coli
grow much slowly
as proteases needed
for proper metabolism

Inducible bacterial promoters
Why not to use constitutive,
always strong promoter?
Induction
Because recombinant (alien) protein
is often toxic for bacterial cell.
Bacteria tend to expel
harmful plasmids
Bacterial grow takes time….

BL(DE3) inducible system and pET vectors (invented in 1984 by Bill Studier, on sale by Novagen)
1) T7 RNA polymerase gene is integrated in chromosome
under the control of a lac promoter and operator
2) lactose analogue, IPTG, causes the host to produce T7 RNA polymerase
3) The E. coli host genome also carries the lacI (repressor) gene
pET23
Gene of interest
is expressed from
strong T7 promoter

Why repressor gene and gene of interest are expressed from different DNA molecules?
Repressor gene expressed from chromosome;
Gene of Interest expressed from plasmid
If too high repressor ? no transcription
(you need to increase expensive IPTG)
If too low repressor ? promoter is leaky
(active without IPTG)
Repressor is in chromosome,
because there it is best kept controlled there
(no plasmid loss, not too high expression)

Where your expressed protein will be located?
Inclusion bodies
(insoluble)
Cytoplasm
(soluble)
Periplasmatic space
(soluble or insoluble)
Secreted (!!)
E.Coli
can not do that

1. Inclusion bodies
(most common case)
-- Inclusion bodies are formed through the accumulation
of folding intermediates
rather than from the native or unfolded proteins.
-- It is not possible to predict which proteins
will be produced as inclusion bodies.
-- Production of inclusion bodies
not dependent on the origin of protein,
the used promoters,
the hydrophobicity of target proteins...

Electron micrograph of an inclusion body of the protein prochymosin in an E. coli cell
Page 116
Protein Folding

Good side of inclusion bodies
inclusion bodies can be accumulated in the cytoplasm
to much higher level (greater than 25%)
than production as soluble form;
2) inclusion bodies is initially isolated
in a highly purified, solid, and concentrated state
by simple physical operation (centrifugation).
3) inclusion bodies have no biological activity.
For toxic proteins it may be the only one available;
4) inclusion bodies are resistant to proteolysis
That results in the high yield of protein production.

SDS-PAGE analysis of recombinant protein produced as inclusion body
hG-CSF
mbel.kaist.ac.krmbel.kaist.ac.kr/research/ protein_en1.html

Recovery of proteins from inclusion bodies
Is not a straightforward process, but road of trials and errors
Solubilization
Refolding
Choice of solubilizing agents,
e.g., urea,
guanidine HCl,
or detergents,
plays a key role
in solubilization
efficiency
-- Refolding is initiated
by reducing concentration
of denaturant used to solubilize IBs.
Guandinium
-- Refolding competes with other reactions,
such as misfolding and aggregation
(both are leading to bad results)
-- Chaperones are helpful in refolding
(including chemical chaperones)

Question of questions –
how to purify your protein?

Diversity of proteins could be exploited
Column chromatography
Matrix particles
usually packed in the column
in the form of small beads.
A protein purification strategy
might employ in turn each of the three kinds of matrix
described below,
with a final protein purification
Of up to 10,000-fold.
Essential Cell Biology:
An Introduction to the Molecular Biology of the Cell

Column chromatography
Different proteins
are retarded to different extents
by their interaction with the matrix,
they can be collected separately
as they flow out from the bottom.
According to the choice of matrix,
proteins can be separated
according to
-- their charge,
-- their hydrophobicity,
-- their size,
-- their ability to bind to
particular chemical groups (!!)
Essential Cell Biology:
An Introduction to the Molecular Biology of the Cell

(A) ION-EXCHANGE CHROMATOGRAPHY
Ion-exchange columns
are packed with small beads
that carry
positive or negative charges
retarding proteins
of the opposite charge.
The association between
a protein and the matrix
depends on the pH
and ionic strength of the solution
passing down the column.
These can be varied in a
controlled way to achieve an effective separation.
Essential Cell Biology:
An Introduction to the Molecular Biology of the Cell

(B) GEL-FILTRATION CHROMATOGRAPHY
Gel-filtration columns
separate proteins
according to their size
on tiny porous beads.
Protein molecules
that are small enough to enter
the holes in the beads
are delayed and travel more slowly
through the column.
Proteins that cannot enter the beads are washed out of the column first.
Such columns also
allow an estimate of protein size.
Essential Cell Biology:
An Introduction to the Molecular Biology of the Cell

(C) AFFINITY CHROMATOGRAPHY
Affinity columns
contain a matrix
covalently coupled to a molecule that interacts specifically
with the protein of interest
(e.g., an antibody, or an
enzyme substrate).
Proteins that bind specifically
to such a column
can finally be released
by a pH change or
by concentrated salt solutions,
and they emerge highly purified.
Essential Cell Biology:
An Introduction to the Molecular Biology of the Cell

Protein
electrophoresis
Essential Cell Biology:
An Introduction to the Molecular Biology of the Cell

www.unizh.chwww.unizh.ch/.../www.unizh.ch/.../Teaching_slide_showswww.unizh.ch/.../Teaching_slide_shows/ Lambda/sld015.htm
www.unizh.chwww.unizh.ch/.../www.unizh.ch/.../Teaching_slide_showswww.unizh.ch/.../Teaching_slide_shows/ Lambda/sld015.htm

Fusion proteins
increase production level
facilitate purification (taq)
detection of expression (GFP fusion)
Redirection of proteins (secretion -> signal peptidases)
Surface display (for screening of libraries)
Tandem arrays (for small peptides, toxic proteins,..)

Most widely used purification strategy – to produce your protein as a fusion
with something easily purifyable
(Invitrogen, Life Technologies, Novagen, QIAGEN):
6xHIS Tag
1. This small addition
rarely affects protein structure
to a significant degree
2. Interaction so strong,
it tolerates denaturing conditions
(could be used for
inclusion bodies purification)

Histidine: a charged aminoacid
The affinity of this interaction is very high
which allows protein purification to 95% in a single step.
Stretch of six histidine residues
interacts with nickel ion
that is tightly bound to a NTA matrix
Nitrilotriacetic acid (NTA) matrix
Histidine

GST – fusion. Principle is the same. Binds to glutation

Require strong
binding to glutathione
Require strong
binding to glutathione
GSTs function catalytically to conjugate glutathione (GSH)
with a wide variety of electrophilic substrates

Glutathione
GST from Schistosoma japonicum
1) Keeps fusion proteins soluble
2) Used for fusion purification
3) Used for protein detection
with GST antibody
26 kDa tag

FUSION PROTEIN BOUND TO GLUTATHIONE SEPHAROSE
Glutathione
GST
FOREIGN PEPTIDE
SEPHAROSE
Purification is simple :
-- WASH COLUMN EXTENSIVELY
-- ELUTE WITH REDUCED GLUTATHIONE
-- RESULTS IN PURE GST FUSION PROTEIN

Some problems of production in E. coli

Some E.coli expression host considerations

Principal factors in bacterial expression

Type of expression vectors

Initiation of Transcription Promoters for Expression in Prokaryotes
In Escherichia coli
- Lac system - plac
- Trp system
- synthetic systems – ptac, ptrc
In Bacillus

The Lac promoter System

The trp promoter system

E. coli Promoter Sites

Synthetic E. coli promoters
-35
-10
ptac -> -35 box from ptrp + -10 box from plac -> pt+ac

Inverted Promoter System (from Salmonella)
-> for very toxic proteins

Bacillus
In 1872, Ferdinand Cohn, a student of Robert Koch, recognized and named the bacterium Bacillus subtilis.
The organism was made to represent a large and diverse genus of Bacteria, Bacillus, and was placed in the family Bacillaceae.
The family's distinguishing feature is the production of endospores, which are highly refractile resting structures formed within the bacterial cells. Since this time, members of the genus Bacillus are characterized as Gram-positive, rod-shaped, aerobic or facultative, endospore-forming bacteria.
Flagellar stains of various species of Bacillus from CDC

Bacillus
Antibiotic Producers: B. brevis (e.g. gramicidin, tyrothricin), B. cereus (e.g. cerexin, zwittermicin), B. circulans (e.g. circulin), B. laterosporus (e.g. laterosporin), B. licheniformis (e.g. bacitracin), B. polymyxa (e.g. polymyxin, colistin), B. pumilus (e.g. pumulin) B. subtilis (e.g. polymyxin, difficidin, subtilin, mycobacillin).
Pathogens of Insects: B. larvae, B. lentimorbis, and B. popilliae are invasive pathogens. B. thuringiensis forms a parasporal crystal that is toxic to beetles.
Pathogens of Animals: B. anthracis, and B. cereus. B. alvei, B. megaterium, B. coagulans, B. laterosporus, B. subtilis, B. sphaericus, B. circulans, B. brevis, B. licheniformis, B. macerans, B. pumilus, and B. thuringiensis have been isolated from human infections.
The Genus Bacillus includes two bacteria of significant medical importance, B. anthracis, the causative agent of anthrax, and B. cereus, which causes food poisoning. Nonanthrax Bacillus species can also cause a wide variety of other infections, and they are being recognized with increasing frequency as pathogens in humans.

Bacillus
Bacillus strains used as production organisms:
- B. subtilis
- B. brevis - B. licheniformis
Transformation systems:
- via competent cells (during transition from vegetative cells -> sporulation, cell can take up DNA (ss) when population reaches a metabolic state called competence)
- protoplast
- bacteriophage-mediated transduction
Vectors:
- replicating plasmids (pUB110, pE194, pC194, pHP13, shuttle vectors)
-> replicating plasmids with temperature-sensitive origin of replication
(replication stops above certain temp. -> pE194 stops above 45ºC)
- integrative vectors (normally shuttle vectors)
Promoters:
- aprE promoter -> induction with onset of sporulation
- amylase promoter -> growth-phase and nutrition regulated promoter (induction at end of exponential growth + repression by glucose)
- sacB promoter (levansurase) -> not regulated
- spac promoter -> hybrid promoter (subtilis phage + lac operator) -> induction with IPTG

Bacillus as expression host

Bacillus as expression host

Products produced in Prokaryotic Systems
Restriction Endonucleases -> produced in E. coli
L- Ascorbic Acid (Vitamin C) -> recombinant Erwinia herbicola (gram-negative bacterium)
Synthesis of Indigo (blue pigment -> dye cotton /jeans) -> produced in E. coli
Amino Acids -> produced in Corynebacterium glutamicum (gram-positive bacterium)
Lipases (laundry industry) -> from Pseudomonas alcaligenes produced in Pseudomonas alcaligenes
Antibiotica (most of them from Streptomyces, other gram-positive bacteria, fungi) -> produced in recombinant Streptomyces and fungi (Penicillium)
Biopolymers (PHB -> biodegradable plastics) -> produced in E. coli (stabilized with parB)

Expression in Eukaryotic Systems
Yeast
- Saccharomyces cerevisiae (baker’s yeast)
- Pichia pastoris
Insect Cells – Baculovirus
Mammalian Cells

Expression in Yeast
Autonomous replicating vectors -> shuttle vectors

Expression in Saccharomyces cerevisiae
Autonomous replicating systems

Expression in Saccharomyces cerevisiae
Integrative systems
Probability for integration higher with linear fragments !

Expression in Saccharomyces cerevisiae

Expression in Saccharomyces cerevisiae

Yeast are efficient secretors !
Secretory expression preferred if:
-> if product toxic
-> if many S-S bonds need to be closed

Expression in S. cerevisiae – Pichia pastoris
Problems with production in S. cerevisiae:
For some proteins production level low
Hyperglycosylation (more than 100 mannose residues in N-glycosylation)
Sometimes secretion not good -> protein stack in cells (periplasma)
S. cerevisiae produces high amount of EtOH -> toxic for the cells -> effects level of production
Advantages of production in Pichia pastoris:
Highly efficient promoter, tightly regulated (alcohol oxidase -> AOX, induced by MeOH)
Produces no EtOH -> very high cell density -> secretion very efficient
Secretes very few proteins -> simplification of purification of secreted proteins

Expression in Pichia pastoris
Integrative systems

Expression in Pichia pastoris

Expression in Pichia pastoris

Expression in Insect cells
Baculovirus:
-> infects invertebrates (insects)
-> in infection cycle 2 forms of baculovirus are formed:
-> single virus particle
-> in protein matrix (polyhedron) trapped clusters of viruses
-> during late stage of infection massive amount of polyhedron produced -> strong promoter
-> polyhedron not required for virus production
-> polyhedron promoter optimal for heterologous protein production in insect cells

Expression in Insect cells
Baculovirus:
-> Autographa californica multiple nuclear polyhedrosis virus (AcMNPV) many used as expression vector
-> Production of recombinant baculovirus:
1. create a transfer vector (E. coli based plasmid with AcMNPV DNA – polyhedrin promoter/terminator + flanking sequences) -> gene of interest cloned downstream of promoter
2. Insect cells are cotransfected with virus (AcMNPV) + transfer vector
-> in some double infected cells -> double crossover event (recombination)
-> produce recombinant virus (bacmid -> E. coli - insect cell baculovirus shuttle vector)
-> cells infected with recombinant virus -> produce plaques (lack of polyhedrin)
3. DNA hydridisation + PCR used to identify recombinant virus
4. Infection of insect cells with concentrated stock of verified recombinant virus
-> 4-5 days later protein harvested

Baculovirus expression system

Why this system?
Insect cells have almost the same posttranslational modifications as mammalian cells
Higher expression level than mammalian cells
Baculovirus expression system

Mammalian cell expression system
1. Why do we use that system?
-> to get full complement of posttranslational modifications on proteins
2. Developed cell lines:
-> short term (transient) expression -> autonomous replicating systems -> viral origins (SV40)
- African green monkey kidney (COS)
- baby hamster kidney (BHK)
- human embryonic kidney (HEK-239)
-> long term (stable) expression -> integration into chromosome -> viral origins
- chinese hamster ovary (CHO)

Mammalian cell expression system

Gene expression in mammalian cell lines
A convenient alternative for setting up mammalian cell facilities – get a comprehensive service from us. We will achieve stable expression of the gene of your interest in mammalian cells.
Customer provides:
- Mammalian vector with the gene (cDNA) to be expressed. We accept plasmid and retroviral vectors
- Sequence of the gene and map of the construct for transfection
Cell line or information about the cell line to be transfected.
Our service includes:
- Transfection of the cells. In case of a retroviral vector, virus production and cell infection
- Antibiotic selection and generation of stable transfected (infected) cell clones. At least 10 independent clones will be selected and grown
- Quantitative assay of the gene (cDNA) expression level in each transfected clone by RNA isolation followed by Northern hybridisation and/or RT-PCR
- Selection of the best expressing clone
- Cell freezing and depositing
- Duration: 3-6 months (depending on the cell growth rate), allow 1month in addition if the cell line is not available in our collections
Customer receives:
- Detailed report on experiments and data obtained.
- Two vials of transfected cells (the best expressing clone)
- We will deposit the transfected cells in our collection as a precaution against accidental loss of the clone.
Price guide:
Price per transfection and selection of at least 10 clones: £3500.