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Applied and Environmental Microbiology, September 2003, p. 5328-5335, Vol. 69, No. 9
0099-2240/03/$08.00+0 DOI: 10.1128/AEM.69.9.5328-5335.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.
Fluorescence-Activated Cell Sorting of Specific Affibody-Displaying Staphylococci
Henrik Wernérus, Patrik Samuelson, and Stefan Ståhl*
Department of Biotechnology, AlbaNova University Center, Royal Institute of Technology (KTH), SE-106 91 Stockholm, Sweden
Received 21 February 2003/
Accepted 26 June 2003

ABSTRACT
Efficient enrichment of staphylococcal cells displaying specific
heterologous affinity ligands on their cell surfaces was demonstrated
by using fluorescence-activated cell sorting. Using bacterial
surface display of peptide or protein libraries for the purpose
of combinatorial protein engineering has previously been investigated
by using gram-negative bacteria. Here, the potential for using
a gram-positive bacterium was evaluated by employing the well-established
surface expression system for
Staphylococcus carnosus.
Staphylococcus aureus protein A domains with binding specificity to immunoglobulin
G or engineered specificity for the G protein of human respiratory
syncytial virus were expressed as surface display on
S. carnosus cells. The surface accessibility and retained binding specificity
of expressed proteins were demonstrated in whole-cell enzyme
and flow cytometry assays. Also, affibody-expressing target
cells could be sorted essentially quantitatively from a moderate
excess of background cells in a single step by using a high-stringency
sorting mode. Furthermore, in a simulated library selection
experiment, a more-than-25,000-fold enrichment of target cells
could be achieved through only two rounds of cell sorting and
regrowth. The results obtained indicate that staphylococcal
surface display of affibody libraries combined with fluoresence-activated
cell sorting might indeed constitute an attractive alternative
to existing technology platforms for affinity-based selections.

INTRODUCTION
Recent advances within the field of combinatorial protein engineering
have led to the development of several complementary technologies
for the selection of novel protein variants from large libraries.
So far, phage display has been the preferred format for directed
evolution efforts (
39), but more recently, other techniques,
such as ribosomal display (
29), covalent display, and different
formats of cell display, have become attractive alternatives
(
46). Cell surface display combined with fluorescence-activated
cell sorting (FACS) constitutes a powerful strategy for isolation
of novel ligands with improved affinity, stability, or enzymatic
activity (
4,
28,
37). The high throughput and quantitative multiparameter
population analysis of modern flow cytometers makes FACS ideal
for protein engineering applications (
7,
46). However, FACS
sorting would only be applicable with cell display systems,
since the phage particles are too small to be sorted with the
present state-of-the-art flow cytometers (
6,
43).
Traditionally, engineering of antibody fragments has been the dominating strategy for generating novel proteins with specific ligand-binding properties (17). More recently, other protein scaffolds have also been investigated as sources for novel affinity ligands (26, 38). One such novel class of affinity proteins, called affibody ligands, i.e., engineered Staphylococcus aureus protein A (SpA) domains, has recently been described (23). Combinatorial libraries were created through simultaneous randomization of 13 amino acid residues. Through the genetic fusion of these libraries to the coat protein III of filamentous phage M13, phage libraries adapted for the selection of novel affinity variants were created. This strategy has been successfully used to select affibody ligands to diverse targets, including Taq DNA polymerase, human recombinant factor VIII, a human apolipoprotein variant, and the G protein of human respiratory syncytial virus (RSV) (15, 23, 25). The same strategy has also been employed to select affibody ligands to immunoglobulins (Igs) for which SpA has no inherent affinity, e.g., human IgA and IgE (12, 30). So far, phage display has been used for selection of affibody ligands, but a number of bacterial expression systems would also be available (3, 18, 33). Regarding bacterial display for protein engineering purposes, combinatorial libraries have so far been displayed only on gram-negative bacteria but inherent morphological properties of gram-positive bacteria would make them an attractive alternative in this context (40). These properties include the observed high viability and robustness of staphylococcal cells in high-speed flow cytometry cell sorting (40, 42) and the convenience of C-terminal anchoring of proteins on the cell surface that is characteristic of gram-positive bacteria (33), which allows insertion of extended sequences without interference with the translocation machinery.
Two previously described systems for cell surface display on the nonpathogenic food-grade bacteria Staphylococcus carnosus (34) and Staphylococcus xylosus (16) have been extensively investigated in various biotechnological applications (43), most frequently for development of live bacterial vaccine delivery vehicles through the display of heterologous immunogens at the cell surface (6, 40). Furthermore, single-chain Fv antibody fragments, as well as IgE- and IgA-specific affibody ligands, have been displayed, creating potential whole-cell diagnostic devices (12, 13). In addition, staphylococci with increased metal-binding capacity have been created through display of polyhistidyl peptides (35), and novel metal-binding proteins have been generated through combinatorial protein engineering approaches (19, 44).
An improved S. carnosus display vector exhibiting enhanced growth characteristics and DNA stability was recently developed (45) for intended use in future display of peptide and protein libraries and subsequent affinity-based selections of fluorescence-labeled target cells by flow cytometry. The observed high viability and robustness of the staphylococcal cells in the flow cytometer might be of considerable importance for this type of application (45). Here, we report the use of a model system employing surface-displayed engineered SpA domains to test the functionality of this S. carnosus display system for the specific enrichment of target cells from a large excess of background cells by flow cytometry. The accessibility and binding specificity of affibody ligands exposed on the surface were analyzed in whole-cell enzyme assays, and target cells were enriched by using single or multiple rounds of sorting and reamplification by growth. Implications for the display of whole affibody libraries and subsequent affinity-based selections of novel binding proteins will be discussed.

MATERIALS AND METHODS
Plasmid constructions.
The
Escherichia coli strain RRI

M15 (
31) was used as the host
strain during plasmid constructions. Gene fragments corresponding
to an engineered IgG-binding SpA domain, Z
wt (
22), or to an
SpA-based affibody binding to the G protein of human respiratory
syncytial virus (RSV), Z
RSV1 (
15), were amplified by PCR. The
5' PCR primer SAPA27 introduced a
BamHI restriction enzyme site
in the upstream region of the affibody sequence. Similarly,
the 3' primer SAPA28 added a
SalI restriction enzyme site in
the downstream region. The generated PCR fragments were ligated
into the surface display vector pSCX
m, which had previously
been digested with
BamHI and
SalI (
45), thus generating the
plasmids pSCXZ
wt and pSCXZ
RSV1, respectively. Positive clones
were identified by PCR screening and verified by DNA sequencing
performed on the Mega-BACE 1000 DNA sequencing system (Amersham
Biosciences, Uppsala, Sweden) by using MegaBACE terminator chemistry
(Amersham Biosciences) in a cycle-sequencing protocol.
Preparation of biotinylated human IgG.
Human IgG was biotinylated by using the EZ-Link Sulfo-NHS-LC-Biotin labeling kit (Pierce, Rockford, Ill.) according to the supplier's recommendations. The unreacted free biotin was removed by Microcon centrifugal filter devices (Millipore Corp., Bedford, Mass.). The final concentration of IgG-biotin was determined by a standard Bradford analysis using bovine serum albumin as a standard.
Evaluation of surface display efficiency and IgG binding.
Overnight cultures of recombinant and wild-type staphylococci were diluted 1:200 in growth medium (containing chloramphenicol when appropriate) and grown at 37°C to an A578 of 1. The cells were harvested and washed twice with phosphate-buffered saline (PBS) supplemented with 0.05% Tween 20 (PBST) (pH 7.5) before being resuspended in PBST to an A578 of 1. One-milliliter aliquots from these suspensions were incubated at room temperature with either biotinylated human serum albumin (HSA) (1.75 µl of biotinylated HSA [2.39 mg/ml] in 1 ml of PBST) or biotinylated IgG (4 µl of biotinylated IgG [11.5 µM] in 1 ml of PBST) for surface expression and binding analysis. The cells were washed twice in PBST prior to resuspension in 1 ml of PBST containing 0.5 units of streptavidin-alkaline phosphatase conjugate (Boehringer, Mannheim, Germany) and then incubated for another 30 min at room temperature. After two additional washings, the cells were diluted 1:10 in substrate buffer (1 M diethanolamine-HCl [pH 9.8], 0.5 mM MgCl2), and five 100-µl aliquots of each cell type were loaded into a microtiter plate before addition of 100 µl of the substrate solution (p-nitrophenylphosphate; Sigma, St. Louis, Mo.). The change in A405 nm was measured for 20 min in an enzyme-linked immunosorbent assay plate reader (SUNRISE, Tecan, Grödingen, Austria).
FACS.
Overnight cultures grown at 37°C were harvested and washed twice in PBS before being resuspended at an optical density at 600 nm of 1 in PBS. Positive (pSCXZwt) and negative (pSCXZRSV1) cell populations were mixed at the desired ratios, and 100-µl aliquots were withdrawn, pelleted, and resuspended in a solution of 14 nM biotin-IgG in PBS. After incubation for 30 min on ice, the cells were washed once with ice-cold PBS before being resuspended in Alexa-Fluor488-streptavidin (Molecular Probes, Eugene, Oreg.) conjugate diluted 1,600x in PBS. Following another incubation for 30 min on ice, the cells were washed and resuspended in PBS at approximately 107 cells per ml and either counted or sorted on the basis of fluorescence intensity with a FACS Vantage SE flow cytometer (Becton Dickinson, Sunnyvale, Calif.). The cytometer was set to enhanced normal-R mode for the single-step enrichments and to enrich for the library simulations. The cells were sorted directly into tryptic soy broth medium and either plated onto chloramphenicol plates or reamplified by incubation overnight and subjected to another round of cell sorting and analysis. After incubation at 37°C for 48 h, the sorted cells were screened by PCR by using primer pairs specific for the genes encoding the Zwt and ZRSV1 variants. The fraction of sorted cells expressing the desired variant could thus be determined.

RESULTS
Background.
In this study, we have explored the possibility of using staphylococcal
surface display and flow cytometry as an alternative to filamentous
phages for affinity-based selection of engineered SpA domains,
the so-called affibody ligands. A previous study demonstrated
that affibody ligands were efficiently displayed with retained
binding specificity on the surfaces of
S. carnosus cells (
12).
Recently, the plasmid vector for surface display on
S. carnosus was significantly improved with respect to genetic stability
with retained surface expression efficiency (
45) in order to
be better suited for library selection applications. This increased
stability should potentially enable the display of whole affibody
ligand libraries at the cell surface. In this study, a model
system consisting of the IgG-binding affibody scaffold, Z
wt (
22,
24), and a previously described affibody, Z
RSV1 (
15), selected
using phage display and specific for the G protein of RSV, was
used for simulated library selections.
Display vectors.
Two novel plasmid vectors were constructed for display of chimeric proteins containing the Zwt or ZRSV1 affibody ligands (15, 24) on the S. carnosus cell surface. In Figure 1, the parental vector, pSCXm (45), as well as the two novel constructs, pSCXZwt and pSCXZRSV1, are schematically depicted together with their encoded gene products as anchored to the staphylococcal cell wall. For simplicity, the recombinant S. carnosus strains were designated Sc:m, Sc:Zwt and Sc:ZRSV1. The pSCXm display vector utilizes the promoter, signal sequence, and propeptide from a Staphyloccocus hyicus lipase for optimized expression and secretion in S. carnosus (20). The lipase propeptide, which is cleaved off in its homologous host, S. hyicus (2), but not in S. carnosus (9), has been extensively studied and proved to be essential for efficient secretion of heterologous gene fusion products in the lipase expression system (8, 32). The vector system also contains the gene fragments X and M from the C-terminal cell wall anchoring part of the SpA gene for covalent anchoring of expressed proteins to the peptidoglycan cell wall (21, 36, 42). In addition, the gene encoding an albumin binding protein (ABP) (27), derived from streptococcal protein G, is also present in the expression vector. The ABP region is expressed as the part of the chimeric surface protein closest to the cell wall-anchoring motifs functioning as a spacer molecule, increasing the accessibility of expressed chimeric proteins at the bacterial surface (41). Also, ABP-containing surface proteins can be extracted from the cell wall by lysostaphin treatment and can subsequently be purified by affinity chromatography on HSA resins (31), utilizing the ABP moiety as an affinity handle. Using this method is a convenient strategy for verifying that the chimeric surface proteins are expressed as full-length proteins and not subjected to degradation. Finally, the ABP tag functions as a reporter molecule in enzyme- and flow cytometry-based whole-cell assays (34, 45) for monitoring expression levels and density of surface-displayed receptors.
Surface expression and IgG-binding analysis.
Before fluorescence-activated cell sorting could be performed,
it was necessary to determine whether the Z
wt and Z
RSV1 domains
were efficiently expressed in a functional form at the cell
surface. In order to analyze the expression levels and accessibility
of the displayed affibody ligands, the ABP region was used as
a reporter molecule in a previously described whole-cell enzyme
assay (
34). Briefly, recombinant and wild-type staphylococcal
cells were grown to early logarithmic phase and incubated with
biotinylated HSA, followed by incubation with a streptavidin-alkaline-phosphatase
conjugate. The presence of surface proteins containing the ABP
domain could then be detected through the addition of a chromogenic
substrate. The results, shown in Fig.
2A, indicate that cells
harboring the pSCXZ
wt or pSCXZ
RSV1 plasmid express ABP-containing
surface proteins at a level similar to that of cells containing
the parental pSCX
m plasmid. In analogy with previous studies,
this would mean that there are approximately 10,000 ABP-containing
proteins displayed per cell, enabling the use of flow cytometry
for sorting for affinity-based selection (
1). The wild-type
S. carnosus cells, not expressing any albumin-binding domains,
were, as expected, negative in this assay (Fig.
2A). The IgG-binding
capacity of the recombinant strains was analyzed in a similar
assay by replacing the biotinylated HSA with biotinylated IgG
in the probing step. The Sc:Z
wt cells were positive in the assay,
while Sc:wt, Sc:
m, and Sc:Z
RSV1 cells demonstrated only background
reactivity (Fig.
2B), which shows that the Z
wt domain may be
efficiently expressed in a functional form on the cell surface
with retained binding specificity. The results also demonstrated
very low levels of unspecific interactions with wild-type
S. carnosus cells and recombinant strains expressing non-IgG-binding
affibody ligands.
Single-step FACS enrichment of Zwt-expressing cells.
Whether working with the screening of combinatorial libraries
or classical protein purification applications, making a calculated
choice between yield and purity is necessary. For library screening
applications, the goal is to obtain the purest possible product
without losing any valuable target cells. Thus, when working
with library selections, the maximum attainable single-step
enrichment factor becomes an important parameter. In an initial
study, we therefore investigated the possibility of quantitative
sorting of Sc:Z
wt cells from a moderate excess of control cells.
Cells expressing a previously selected affibody ligand, Z
RSV1,
capable of specific recognition of the G protein of RSV served
as a relevant nontarget background population. Specifically,
overnight cell cultures of Sc:Z
wt target cells were mixed with
Sc:Z
RSV1 control cells at ratios of 1:1, 1:100 and 1:1,000.
The cell mixtures were incubated with biotinylated IgG and an
Alexa-Fluor
488-streptavidin conjugate before being analyzed
and sorted on the basis of fluorescence. Since these initial
sortings aimed at obtaining a high degree of purity in a single
sorting round, a relatively narrow sorting gate was set to minimize
the number of nontarget background cells being sorted. The fraction
of the total cell population that was sorted corresponded to
approximately 50, 1, and 0.1%, respectively, for the 1:1, 1:100,
and 1:1,000 mixtures (data not shown). The cells were collected
and filtered through a sterile filter and applied to chloramphenicol
plates. To verify that the sorted cells were indeed Sc:Z
wt,
PCR primer pairs specific for either Z
wt or Z
RSV1 were used
for clone-specific PCR amplification and screening purposes
directly on staphylococcal colonies. The results, presented
in Table
1, clearly indicate that essentially quantitative sorting
of target cells may be obtained from a moderate excess of background
cells in a single sorting round. For the 1:1 mixture, 100% of
the analyzed cells were identified as Sc:Z
wt, while the numbers
for the 1:100 and 1:1,000 mixtures were 95 and 80%, respectively.
This means there was a 571-fold enrichment of Z
wt-expressing
target cells in a single sorting round for the 1:1,000 mixture.
Furthermore, the high viability observed for the sorted staphylococcal
cells suggests a possible advantage of using gram-positive bacteria
for cell-sorting applications. More than 95% of the analyzed
and sorted cells were capable of growth on chloramphenicol plates
(Table
1), indicating that the inherent structure of the staphylococcal
cell wall, i.e., the thick peptidoglycan layer, indeed seems
to improve ability to withstand the elevated shear forces acting
on the individual cells in the flow cytometer.
Sorting of very rare target cells from a large background.
The possibility of also using FACS for the isolation of very
rare target cells from a large excess of background cells was
evaluated.
S. carnosus cells expressing surface displays of
Z
wt or Z
RSV1 affibody ligands were mixed at a ratio of 1:100,000
and labeled with biotinylated IgG and Alexa-Fluor
488-streptavidin
conjugate to create a simulated library situation. In this experiment,
the starting mixture was incubated with the fluorescence-labeled
probes, sorted on the basis of fluorescence, and enriched through
multiple rounds of cell sorting and amplification by overnight
growth (Fig.
3). Since the initial number of positive cells
in this experiment was very small, a wide sorting gate was set
so as not to lose any valuable target cells. Initially, approximately
0.2% of the control Sc:Z
RSV cells fell within the sorting window
(Fig.
4C), thus ensuring that most of the target cells were
effectively sorted in the first sorting round. One million cells
from the input mixture were run through the flow cytometer,
and Z
wt-expressing target cells that fell within the sorting
window were collected and grown overnight in fresh medium and
re-sorted. The cell fluorescence distribution after two rounds
of sorting and regrowth are shown in Fig.
4C through E, and
that of the positive and negative control populations is shown
in Fig.
4A and B. The bar in each graph represents the sorting
gate setting, i.e., the minimum fluorescence intensity defined
as a positive event, with the results for nonstained Sc:Z
RSV1 bacterial cells displayed to the left in the histograms and
the results for cells exposing Z
wt-containing proteins on their
surfaces shifted to the right. Approximately 26% of the cells
fell within the positive window (Fig.
4E), which corresponds
to a more-than-25,000-fold enrichment of target cells in only
two rounds of cell sorting. The identities of the sorted cells
were further analyzed by PCR screening as before, confirming
the identity of selected cells (data not shown). These data
demonstrate that specific enrichment of rare target cells can
be efficiently achieved by FACS sorting by using the above staphylococcal
display system. Importantly, the observed enrichment is not
due to a growth advantage of the Z
wt-expressing
S. carnosus cells, since repeated regrowth of the starting mixture without
in-between cell sorting did not result in any significant bias
when analyzed by PCR screening using Z
wt-specific primers (data
not shown).

DISCUSSION
In this study, we have demonstrated the possibility of using
staphylococcal surface display and flow cytometry as a potential
alternative to filamentous phages for the specific and quantitative
isolation of novel affinity pairs from surface-displayed affibody
libraries. Recombinant
S. carnosus strains with engineered SpA
domains specific for IgG or the G protein of human RSV exposed
on the surface were created. The chimeric surface proteins were
shown to be expressed in an accessible form with retained binding
specificity at the staphylococcal surface by an enzyme assay
based on the ABP domain. Also, affibody-expressing target cells
could be sorted essentially quantitatively from a moderate excess
of nontarget staphylococci in a single sorting round by using
a high-stringency sorting mode. Furthermore, by using a simulated
library situation, a more-than-25,000-fold enrichment of target
cells was achieved through only two successive rounds of cell
sorting and regrowth. This indicates that real affinity-based
selections from surface-displayed affibody libraries would be
feasible. In addition, the staphylococcal cells seem to be highly
suited for flow cytometry applications, since they also demonstrate
a high degree of viability after high-speed sorting. More than
95% of the sorted cells grow well on chloramphenicol plates
after sorting. This capability is probably due to their high
resistance to shear forces related to the thick peptidoglycan
cell wall.
One important advantage of cell-based display systems compared to monovalent phage display is the apparent lack of avidity effects. While phage display systems based on pIII fusions rely on single molecular binding events, a so-called monovalent display, the staphylococcal display system described here typically expresses around 10,000 copies of the displayed protein per cell. This means that random variation in expression levels or stability should not interfere with library selections. Furthermore, the presence of the ABP reporter molecule in the surface chimeras would make it possible to normalize ligand binding by taking into account the number of surface proteins per cell, avoiding artifacts related to expression biases when working with small differences in affinity. This would be of utmost importance if working with real library selections involving fine affinity discrimination of library members.
One obvious challenge when using cell-based systems, like bacterial or yeast display (46), rather than in vitro-based ribosomal display or oil-water emulsion techniques (14) is the limited library size that can be obtained due to restrictions in the transformation step. For the staphylococcal display system described here, the routinely obtained transformation frequency using present transformation methods would be around 105 to 106 transformants per µg of DNA (10), comparable to the numbers reported for yeast and mammalian cell-based display systems (5). Nevertheless, one important application that obviates the need for very large libraries is the use of the S. carnosus system in affinity maturation strategies, where small biased libraries can be constructed on the basis of previously selected binders, thus eliminating the need for very large libraries (11, 25). In the future, it would therefore be interesting to test the staphylococcal display system described here for the affinity maturation of previously selected affibody ligands.

ACKNOWLEDGMENTS
We are grateful to George Georgiou for letting us conduct initial
model experiments in his lab.
This work was financially supported by Cell Factory for Functional Genomics, a program funded by the Swedish Foundation for Strategic Research. P.S. was supported by a postdoctoral fellowship from the Wenner-Gren Foundation.

FOOTNOTES
* Corresponding author. Mailing address: Department of Biotechnology, AlbaNova University Center, Royal Institute of Technology (KTH), SE-106 91 Stockholm, Sweden. Phone: 46 8 553 783 29. Fax: 46 8 553 784 81. E-mail:
stefans{at}biotech.kth.se.


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Applied and Environmental Microbiology, September 2003, p. 5328-5335, Vol. 69, No. 9
0099-2240/03/$08.00+0 DOI: 10.1128/AEM.69.9.5328-5335.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.
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