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Engineering proteins to facilitate
bioprocessing
Per-Ake Nygren, Stefan St hl and Mathias Uhl n
Genetic engineering is now being applied to aid the purification of recombinant
proteins. The addition of specifically designed tags or the modification of sequences
within the target-gene product has enabled the development of novel strategies for
downstream processing that can be employed for efficient recovery of both native
or modified proteins. This article discusses novel trends in genetic engineering that
aid the bioprocessing of recombinant proteins.
A decade has passed since the first example of the use
of gent, fusions for affinity purification of recombinant proteins was reported 1. In the intervening years,
a large number of affinity-fusion systems have been
developed 2,3 and literally thousands 0£ gene fusions
have been used for affinity purification. However, the
use of gene technology to engineer proteins to facilitate bioprocessing has not yet been widely used for the
production of recombinant proteins on an industrial
P-A. Ny~,ren, S. Stahl and M. Uhl{n are at the Department of
Biochemistry and Biotechnology, Royal Institute of Technology, S- 1 O0
44 Stockholm, Sweden.
BTECH MAY 1994 (VOL12)
scale. The main reason for this is probably due to the
demand for the 'first generation' of recombinant proteins to be produced in their native form. Gene-fusion
strategies introduce an additional problem into the
downstream processing, since a site-specific cleavage
is required to remove the affinity tag.
This review discusses the application of genetic
engineering to bioprocessing, including the use of
small affinity tags and the rational design ofgene products in terms of their isoelectric point, solubility or
partitioning coefficient to simplify the recovery of
recombinant proteins. In addition, recent improvements in enzymic-cleavage methods are addressed.
© 1994, Elsevier Science Ltd
185
reviews
Table 1. Examples of commercial systems used in the production of recombinant proteins
fused to affinity tails a
Fusion partner
Size
Ligand
Elution condition
Supplier(s)
ZZ
His tail
14 kDa
6-10 aa
IgG
Ni2÷
Low pH
Imidazole
Strep-tag
PinPointTM
MBP
GST
FlagTM peptide
10 aa
13 kDab
40 kDa
25 kDa
8 aa
Streptavidin
Streptavidinc
Amylose
Glutathione
Specific mAb
Iminobiotin
Biotin
Maltose
Reducing agent
Low calcium
Pharmacia, Sweden
Novagen, USA; Invitrogen, USA;
Qiagen, USA
Biometra, Germany
Promega, USA
New England Biolabs, USA
Pharmacia, Sweden
IBI Kodak, USA
~Abbreviations:aa, amino acids; His, histidine;GST, glutathione-S-transferase;MBP, maltose-bindingprotein.
bEncodes a domain biotiny]atedin vivo in Escherichia coil
CMonomericstreptavidin.
Despite the initial reluctance to apply this technology on a commercial scale, the demand to reduce
capital costs and operating times for downstream processing will motivate wider use of gene-fusion technology in the future, since it will be possible to integrate several unit operations by rational genetic design
of the protein being produced.
Fusions to facilitate protein purification
A large number of affinity tails have been developed
to facilitate the downstream purification of recombinant proteins, and these permit several alternative
purification protocols. However, factors such as proteolytic stability, solubility, the ability of the protein to
be secreted, protein folding and the purification conditions have to be taken into consideration when
choosing a suitable expression strategy for a specific
protein. In particular, proteins produced as inclusion
bodies must be refolded, or at least solubilized, prior
to purification via affinity tails. Kits based on several
of these tails have been produced commercially, in
which expression vectors are manufactured together
with the corresponding affinity resin. A selection of
these systems is shown in Table 1.
One of the best-characterized systems, staphylococcal protein A and its derivative ZZ, has been used
successfully in several different hosts such as bacteria <S,
yeast<7, Chinese hamster ovary (CHO) cells (E Lind,
unpublished) and insect cells 8. The need for a low
pH (pH 3 is routinely used) for elution of the protein
from the affinity column can be circumvented by
the use of competitive elution strategies based on
engineered competitor proteins that can be removed
efficiently from the eluate mix (J. Nilsson, M. Uhl6n
and E A. Nygren, unpublished). The human p olyclonal IgG used as the ligand in this system can be
replaced by recombinant Fc fragments, thus avoiding
the use of a human serum protein in the purification
protocol.
The Strep-tag system9 uses a short (10-residue) peptide sequence with affinity for streptavidin which, in
contrast with the natural ligand, biotin, can be eluted
using mild conditions (11rim iminobiotin). To date,
only fusions with this tag placed C-terminally have
been described.
A related system is PinPont TM, which utilizes the
in vivo biotinylation by Escherichia coli of a 13kDa
sequence attached to the target protein, combined
with affinity purification of the fusion protein on
monomeric streptavidin, thus enabling mild elution
conditions (5 mm biotin) to be employed. Recently, a
Lac-repressor-fusion-based peptide library was developed where a 13-amino-acid sequence was found
to be sufficient to mimic efficiently the much larger
natural domain normally recognized by the biotinylating enzyme 1°. Both N- and C-terminal fusions to
the tail have been demonstrated to be functional. The
use of this much smaller tag would result in a higher
product: tail ratio.
The FlagTM system is based on the Ca2+-dependent
binding ofa monoclonal antibody (mAb) to an eightamino-acid peptide containing an enterokinase recognition site fused N-terminally to the target protein.
The use of a low-Ca 2+ buffer as the eluant makes this
system suitable for the recovery of sensitive target proteins. However, for large-scale applications, the cost
of the affinity resin must be taken into consideration.
Fusions to maltose-binding protein (MBP) are also
eluted using gentle conditions (sugar), and can be produced both intracellularly or, alternatively, as secreted
proteins.
Polyhistidine tails are widely used as affinity tags and
offer the possibility of purifying the recombinant
protein by immobilized-metal-ion affinity chromatography (IMAC) under denaturing conditions, such
as 6M guanidine hydrochloride or 8M urea 11,12. An
intracellular expression system based on fusion to
glutathione-S-transferase (GST), relies on the affinity
of GST for glutathione .3. Numerous examples have
shown that high-level cytoplasmic production of
heterologous proteins is frequently associated with
precipitation of the product into insoluble inclusion
bodies. However, if the target protein is fused to a
highly soluble partner such as the GST moiety, up to
45% of the total cell protein can be produced intracellularly in E. coli in a soluble form TM.
In general, there appears to be a trend to design or
select short affinity tails, particularly as the affinity tag
can then be genetically fused to the target gene by
polymerase chain reaction (PCR) techniques (Fig. 1).
TIBTECHMAY1994(VOL12)
186
reviews
Handle
primer
Target gene
Cleavage site
for processing
Iral
[[
Primer
PoR
Target gene
[ Gene expression
Figure 1
Fusion of a target protein to an affinity tag to enable simplifiedrecovery using polymerasechain reaction (PCR).The tag sequenceis introduced via a non-complementaryhandle sequence in one of the PCR
primers used for amplification. This PCR-based strategy for subcloning the gene fragment into an expressionvector might simplify
conventionalengineeringof the gene product for adaptationto downstream bioprocessing.
native N-terminal after cleavage, and has been used
successfully for site-specific cleavage of a number of
fusion proteins ls,19,25. H64A subtilisin has not yet
been commercialized, but other available enzymes,
such as enterokinase, thrombin and factor Xa, which
all leave native N-terminals have, in several cases, also
been shown to give high cleavage yields (Table 2).
However, these proteases, which all cleave after a basic
residue, sometimes display nonspecffic cleavages.
Thus, the yield of native protein can be dramatically
decreased. However, the IgA-protease from Neisseria
2onorrhoeae 26, which requires a proline in the P2' (see
footnote*) position, has been shown to be very efficient2°. This enzyme has the additional advantage of
being produced as a recombinant protein in E. coli,
thus simplifying its production and purification.
For certain applications, it might be convenient to
perform the site-specific cleavage with the fusion protein still immobilized on the affinity column. Using
this strategy, the DNA-binding domain of the glucocorticoid receptor fused to protein A (Ref. 27), and
mutants of the bovine pancreatic trypsin inhibitor
(BPTI) (R.ef. 28) were produced without the need to
elute the protein prior to cleavage. The latter case is
an elegant example of the integration of unit operations, since the BPTI mutants were affinity purified
on a chymotrypsin column, which also processed a
chymotrypsin recognition site in the fusion protein.
Integration of unit operations
This trend might be further enhanced by novel phagedisplay and other powerful selection techniques,
which have the potential to provide a rich source of
short tails that are suitable for use in purifying and
detecting recombinant proteins. For industrial production, the economic aspects of systems based on
proteinaceous ligands must be considered, for reasons
such as the need for 'cleaning-in-place' (CIP), in order
to decontaminate columns for repeated use.
Site-specific removal of affinity handles
When a native gene product is desired, site-specific
cleavage of the expressed fusion protein has to be performed. A vast number of cleavage methods, both
chemical and enzymic, have been investigated for this
purpose 2,3,15. Table 2 describes some of the more
widely used cleavage methods that have been shown
to be relatively efficient and specific. To illustrate the
practical conditions for such cleavages, a representative exdhaple for each method is presented.
Chemical-cleavage methods have a rather low specificity and the relatively harsh cleavage conditions can
cause chemical modification of the released products 1s'22. Such methods are, therefore, primarily used
in the preparation of peptides and smaller proteins.
However, for certain products, chemical-cleavage
methods have been used successfully, and they offer
the attraction of being cost-effective and relatively
easy to scale up 23.
Among the enzymic methods, H64A subtilisin24
holds great promise, since it is highly specific, leaves a
IBTECH MAY 1994 (VOL 12)
An important part of modern biotechnology is to
develop simplified schemes for the production and
downstream processing of recombinant proteins by
the integration of unit operations 29. Gene-product
design can be used in several ways to implement such
schemes, i.e. by influencing the yield and localization
of the product, as well as adapting the gene product
by fusion technology to specific unit operations suitable for large-scale downstream processing.
The isoelectric point (pI) of a protein can be altered
by the addition of charged amino acid residues,
enabling the use of easily decontaminated ionexchange-chromatography media in the separation
process 3°. Recently, an expanded-bed adsorption procedure was used for efficient recovery of a secreted
recombinant fusion protein directly from a crude fermenter broth, without prior cell removal. The fusion
protein was designed to have a relatively low pI to
allow anionic exchange adsorption at pH 5.5, at
which most host E. coli proteins are not adsorbed. This
strategy enabled integration of the cell-separation step
with ion-exchange adsorption of the gene product
with simultaneous volume reduction (Fig. 2A). An
overall yield of > 90% was obtained, including a subsequent affinity-chromatography polishing step 31.
An alternative strategy to simplify downstream processing was investigated by Kthler and co-workers 32,
* T h e cleavage w i n d o w for a protease is defined as: P 3 - P 2 - P I , ~ P I ' P2'-P3', w h e r e cleavage occurs at the b o n d b e t w e e n the P l and P I '
residues.
187
reviews
Table 2. Examples of methods for site-specific cleavage of fusion proteins a
Cleavage
agent
Chemical
agents
Hydroxylamine
CNBr
Fusion
example
Cleavage
sequence b
Cleavage
conditions
Ratio c
(enzyme : substrate)
ZZ-IGF-I
ZZ-IGF-II
Asn ~ Gly
Met ~
6h, 45°C, pH9.2
12h, 25°C, O. 1 M HCI
2M
50 : 1 (molar excess)
FlagTm-lL-2
ZZ-PTH
MS2-CD8
MBPparamyosin
ZZ-PTH
(Asp) 4 Lys ~ X
Phe Ala His Tyr ~ X
Pro Pro ~Thr Pro
lie Glu Gly Arg ~ X
16h, 37°C, pH 8.0
4h, 37°C, pH 8.6
lh, 37°C, pH 7.4
lh, 25°C, pH 7.2
1 : 20 [w/w]
1 : 20
1:100
1 : 100
Phe Phe Pro Arg ~ X
6h, 20°C, pH3 6.5
1 : 100
Site-specific
cleavage (%)
Ref.
80
80
16
17
90
100
100
100
18
19
20
21
70
19
Enzymes
Enterokinase
H64A Subtilisin
IgA protease
Factor Xa
Thrombin
aAbbreviations: CNBr, cyanogen bromide; IGF-I, insulin-like growth factor I; IL-2, interleukin 2; PTH, parathyroid hormone; MBP, maltose-binding protein.
bThe cleavage sequence shown here relates to the specific example shown. For some of the enzymes, alternative sequences are also reported to be
functional.
CThew/w ratio only relates to the enzymic cleavages. For the CNBr cleavage, the ratio is defined as mole CNBr:mole Met residues.
in which recombinant technology was applied to alter
the partitioning properties of a gene-fusion product,
enabling it to be recovered efficiently by aqueous twophase extraction as a primary purification step. An
attractive approach to simplify the recovery of products that may be produced with modified primary
sequences, e.g. industrial enzymes, would be to alter
the partitioning properties by substituting tryptophan
residues for one or more surface amino acid residues
that are not involved in biological activity 32. This type
of protein engineering will probably be used in the
future to reduce production costs for bulk proteins.
A third example of how unit operations can be
integrated by careful design of the gene product
and the recovery process was recently demonstrated
for the production of native human insulin in
E. coli [R Jonasson, j. Nilsson, E. Samuelsson and
M. Uhl6n, unpublished]. Human proinsulin was fused
genetically to an IgG-binding affinity tail (ZZ)
(Fig. 2B), and recovered from inclusion bodies by
solubilization and refolding of the intact fusion
protein. Native insulin, composed ofcysteine-bridged
A and B chains, could be released by a single-step
trypsin treatment that cleaved off the ZZ-tail at the
same time as processing the C-peptide.
a
I
Fermentation
Fermentation
Cell separation
Concentration
Chromatography I
Chromatography II
Affinity
Chromatography I11
chromatography
Polishing
Polishing
I
b
z z
IgG-binding
Human proinsulin
Enhanced solubility for in vitro refolding
The recovery of biologically active or native proteins
by in vitro refolding from insoluble inclusion bodies is
often hampered by the aggregation of the prodttct
during the procedure, leading to low overall yields. To
make the procedure more efficient, several improved
protocols have been developed, including the addition
of'folding enhancers', such as L-arginine 33-35, chaperones 36, polyethylene glycol (PEG) (Ref. 37), or even
monoclonal antibodies 3s. Alternatively, the protein
itself can be engineered to facilitate the refolding. The
presence of hydrophilic peptide extensions, during the
refolding can dramatically improve the folding yield,
probably by conferring a higher overall solubility
Figure 2
Examples of integration of unit operations enabled by genetic design of the product.
(a) Several unit operations can be integrated by engineering the product to enable it
to be recovered by an expanded-bedadsorption procedure. The left-hand panel lists
the number of unit operations that are normally included in the downstream processing of a gene product. Several chromatographic separation steps based on ionexchange, size exclusion, hydrophobic interaction etc., might be utilized. The righthand panel illustrates that unit operations such as cell separation, concentration and
chromatographic recovery can be combined into a single procedure. (b) The fusion
protein from which native insulin can be recovered by a single trypsin treatment that
simultaneously releases the ZZ-tail and processes the C-chain. To obtain completely
native insulin, the C-terminal arginines of the B-chain are processed using carboxypeptidase. The arrows indicate processing sites for trypsin.
TIBTECHMAY1994(VOL12)
188
reviews
on the protein 34. Samuelsson and co-workers 39 showed
that the reshuffling of misfolded disulfides in recombinant insulin-like growth factor I (IGF-I) was greatly
facilitated by the highly soluble Z Z fusion partner.
Compared with unfused IGF-I, the fusion could
be successfully refolded at >100-fold higher concentrations (1-2 mg ml<), without the formation
of precipitates 4°.
Second generation therapeutic products
Protein engineering offers the possibility of producing 'second-generation' therapeutics (compounds
modified compared with the native molecule) to
enhance therapeutic values and/or to facilitate production and purification processes. For example, tissue
plasminogen activator (tPA) naturally comprises several
discrete domains with different functions. However, a
non-glycosylated deletion variant produced in E. coli
by in vitro refolding showed improved thrombolytic and
pharmacokinetic characteristics compared with the
parent molecule34,4E Genetic fusion to one or more
moieties can confer additional characteristics on a protein. For example, fusion to fragments of mAbs enables
in vivo targeting of toxins42, while fusion to stable protein domains can increase serum hail-life43,44. By using
such protein-engineering techniques, the need for
chemical linking to achieve the combined activities is
circumvented. For vaccine development, coherent antigens can be produced where carrier and/or immunostimulating properties are added to the immunogen by
fusion to suitable moieties 45.
Conclusions
During the past decade, an increasing number of
applications involving genetically engineered proteins
have emerged. Integrated bioprocesses based on
rational design have the advantage that the production and recovery of recombinant proteins, such as
pharmaceuticals or industrial enzymes, can be achieved
with high yields and at relatively low costs. Charge
distribution, solubility, pI and other biophysical parameters can be altered and employed during downstream
processing. This 'biotech' approach to protein engineering can also be used to adapt the enzyme for directed
immobilization 46,47 in, for example, enzyme reactors
and biosensors.
Acknowledgements
We thank Rainer Rudolph and Peter Lind for valuable information and stimulating discussions.
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