Download Development of a protein microarray using sequence

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Biochemical and Biophysical Research Communications 329 (2005) 1315–1319
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Development of a protein microarray using sequence-specific
DNA binding domain on DNA chip surface
Yoo Seong Choi a, Seung Pil Pack b, Young Je Yoo
a
a,*
School of Chemical and Biological Engineering, Seoul National University, Seoul 151-742, Republic of Korea
b
International Innovation Center, Kyoto University, Kyoto 606-8501, Japan
Received 23 December 2004
Abstract
A protein microarray based on DNA microarray platform was developed to identify protein–protein interactions in vitro. The
conventional DNA chip surface by 156-bp PCR product was prepared for a substrate of protein microarray. High-affinity sequencespecific DNA binding domain, GAL4 DNA binding domain, was introduced to the protein microarray as fusion partner of a target
model protein, enhanced green fluorescent protein. The target protein was oriented immobilized directly on the DNA chip surface.
Finally, monoclonal antibody of the target protein was used to identify the immobilized protein on the surface. This study shows
that the conventional DNA chip can be used to make a protein microarray directly, and this novel protein microarray can be applicable as a tool for identifying protein–protein interactions.
2005 Elsevier Inc. All rights reserved.
Keywords: Protein microarray; Biochip; DNA chip; DNA binding domain
The development of the arrays of immobilized biological compounds and gene expression studies by the
method has been significant in post-genomic era. However, protein microarray technology beyond DNA chips
is required to characterize proteomes, because mRNA
level and protein expression do not necessarily correlate
[1]. Protein microarray technology has been applied for
antibody–antigen, protein–protein, protein–lipid, and
protein–small-molecule interactions, and it has shown
great potential in proteomics, drug discovery, and diagnostics [2,3]. Considering that immobilized proteins
have to be kept functionally active in a native conformation and the arrays will be used for basic and applied
proteome research in a high-throughput manner, major
hurdles have been the ability to generate the necessary
expression clones, and the expression and purification
of proteins in a high-throughput fashion [4], and the
*
Corresponding author. Fax: +82 2 887 1659.
E-mail address: [email protected] (Y.J. Yoo).
0006-291X/$ - see front matter 2005 Elsevier Inc. All rights reserved.
doi:10.1016/j.bbrc.2005.01.167
conformation and orientation of binding proteins on
chip surface are also important [5,6].
A variety of means of protein attachments based on
the approaches such as adsorption, covalent cross-linking, diffusion, and affinity binding were reported. Protein attachment through highly specific affinity
interactions among them is deemed appropriate for
high-throughput approach and protein orientation in
which proteins fused with a high-affinity tag at aminoor carboxy terminus are linked to the surface of the chip
via this tag [7]. Each of the open reading frames was
cloned into a yeast expression vector, and expression
and purification was performed directly in microtiter
plates. Oriented immobilization of each protein was
conducted into the modified chip surface such as glutathione surface, Ni2+ chelating surface by biological
affinity without any modification of the protein [4,8].
Self-assembling protein microarrays, which were generated by in situ immobilization of the epitope tagged protein in vitro translated from each cDNA spot, were also
reported [9].
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Surface for protein immobilization is also important
to prepare protein microarray. Several different coatings
have been published, which can be divided into two
types: gel-coated surfaces and non-gel-coated glass or
plastic surfaces [10]. Proteins do not provide a uniform
outer surface unlike DNA, and proteins tend to unfold
when immobilized onto a support to allow internal
hydrophobic side chains to form hydrophobic bonds
with the solid surface [11]. Until now, DNA chip technologies were well established in a measure commercially available. It is known that the experimental
procedure has been shown as a standard tool in the
chip-based array system from the ligand immobilization
to the detection of the sample. Especially, existing techniques for immobilizing nucleic acids including oligonucleotide and cDNA on solid surface were well studied
and optimized. However, although DNA microarrays
are well established in high-throughput fashion, the surfaces typically used with DNA are not easily adaptable
to proteins, owing to the biophysical differences between
the two classes of bioanalytes [12].
In this manner, a protein microarray based on DNA
chip platform and specific affinity of protein–DNA
interaction was described to identify protein–protein
interaction. The conventional DNA microarray surface
was prepared for a substrate of protein microarray.
High-affinity sequence-specific GAL4 DNA binding domain (GAL4 DBD), whose dissociation constant lies in
nanomolar range (109), was introduced to the protein
microarray as a linker of target model protein by amino
terminus fusion [13]. Enhanced green fluorescent protein
(EGFP) as a model protein was immobilized site-specifically on the DNA chip. The monoclonal antibody of
EGFP was applied to identify protein–protein interaction. This study shows that the conventional DNA chip
platform can be used to make a protein chip directly,
and the tool is possible to obtain identical protein orientation by oriented immobilization with no protein modification, and can be used to purify the expressed
proteins by biomolecular affinity in high-throughput
fashion.
GGC CGA ATT CGA TAC AGT CAA CTG TCT TTG-3 0 , respectively. EcoRI and HindIII restriction sites were introduced into the
EGFP fragment by the primers: 5 0 -GGC GGC GAA TTC GGT GAG
CAA GGG CGA GGA GCT-3 0 and 5 0 -GGC GGC AAG CTT CTT
GTA CAG CTC GTC CAT GCC-3 0 , respectively. And the amplified
sequences were identified by sequencing. Through the PCR products
were digested with NdeI/EcoRI and EcoRI/HindIII, respectively, the
fusion protein expression vector (Fig. 1A), pEGEL which encodes the
GAL4 DBD and EGFP fusion protein, was constructed by cloning
into the expression plasmid pET23b (Novagen). The expression vector
pEGFP was also cloned to produce EGFP protein based on the same
vector system with 5 0 NdeI and 3 0 HindIII restriction sites by the following primers: 5 0 -CCG GTG GCC CAT ATG GTG AGC AAG
GGC GAG-3 0 and 5 0 -GGC GGC AAG CTT CTT GTA CAG CTC
GTC CAT GCC-3 0 , respectively.
Protein expression and purification. The recombinant plasmids were
introduced into E. coli BL21(DE3), and the E. coli cells bearing the
plasmids were grown in LA medium at 37 C, 200 rpm and induced
with 0.8 mM IPTG: in the case of E. coli cells including pEGEL,
ZnSO4 was also added to a final concentration of 20 lM. The cells
were harvested by centrifugation and resuspended in a lysis buffer
(100 mM NaH2PO4, pH 8.0, 300 mM NaCl, 20 lM ZnSO4, 0.05%
Tween 20, and 10 mM imidazole) after 20 C, 200 rpm, 20 h post-induction. The cells were then disrupted by sonication and the supernatants were prepared for protein purification.
The cell supernatant was applied to the Ni–NTA agarose resin
(Qiagen) and equilibrated in the lysis buffer at 4 C for 1 h. The lysate–
Ni–NTA mixture was loaded into a mini-column and washed five
times with four column volumes of a buffer (100 mM NaH2PO4, pH
8.0, 300 mM NaCl, 20 lM ZnSO4, 0.05% Tween 20, and 20 mM
imidazole). The fusion protein was eluted with the elution buffer
(100 mM NaH2PO4, pH 8.0, 300 mM NaCl, 20 lM ZnSO4, 0.05%
Tween 20, and 250 mM imidazole). The final purity of the proteins was
assessed by sodium dodecyl sulfate–polyacrylamide gel electrophoresis
(SDS–PAGE) and protein concentrations were determined using the
modified Lowry reagent (Sigma). Finally, the buffer of the proteins was
changed into a binding buffer (20 mM Hepes, pH 7.5, 50 mM NaCl,
5 mM MgCl2, 20 lM ZnSO4, 0.05% Tween 20, and 20% glycerol).
DNA surface preparation. 5 0 -Amino modified PCR product of the
yeast upstream activating sequence including GAL4 binding sites
(UASG) was obtained from Saccharomyces cerevisiae genomic DNA.
The oligonucleotides, 5 0 -amino-CTC ATT GCT CAG CTG AAG
TAC GGA TTA GAA GCC-3 0 and 5 0 -TGT AGA AGA TCT ATT
Materials and methods
Microorganisms and cultivation. Escherichia coli Top10 and E. coli
BL21(DE3) were used as host cells for gene cloning and overexpression
experiments, respectively. LB medium was used for the growth of E.
coli Top10 and BL21(DE3). LA medium and LK medium, which were
supplemented with 50 lg/mL ampicillin and 50 lg/mL kanamycin into
LB medium, respectively, were used for the growth and selection of E.
coli transformants. All E. coli strains were grown at 37 C, 200 rpm.
Genetic manipulation. The DNA fragments of GAL4 DBD (amino
acid 1–147) and EGFP were obtained by PCR from pGBKT7 plasmid
vector (Clontech) and pEGFP-1 (Clontech), respectively. NdeI and
EcoRI restriction sites were introduced into the 5 0 and 3 0 ends of the
GAL4 DBD fragment using the following primers: 5 0 -GCC GCC CAT
ATG GCT AGC AAG CTA CTG TCT TCT ATC-3 0 and 5 0 -GGC
Fig. 1. Schematic diagram of the expression vector and the purification of the expressed proteins. (A) DNA fragment encoding GAL4
DBD and EGFP was inserted between NdeI and HindIII. (B) The
EGFP protein and the GAL4 DBD/EGFP fusion protein were
expressed and purified by Ni–NTA affinity chromatography. Lane 1,
protein marker; lane 2, EGFP; and lane 3, GAL4 DBD/EGFP.
Y.S. Choi et al. / Biochemical and Biophysical Research Communications 329 (2005) 1315–1319
GTT CGG AGC AGT GCG GCG-3 0 , were used as PCR primer. The
amplified fragments were purified using DNA purification kit (Qiagen)
and prepared in 3· SSC buffer (450 mM NaCl, 45 mM sodium acetate,
pH 7.0). Silylated glass slides (Telechem) were immersed into the
solution of the 5 0 -amino modified PCR product for 8 h at room temperature. To remove non-covalently bound DNA, the slides were
washed in 2· SSC, 0.2% SDS buffer, and 1· SSC buffer, and free
aldehyde groups were blocked in sodium borohydride solution, washed
thoroughly with deionized distilled water, and stored in the dark at
4 C [14].
Electrophoretic mobility shift assay (EMSA). PCR product of
UASG, which included four binding sites of GAL4 DBD, was obtained
from S. cerevisiae genomic DNA using the primers of 5 0 -CTC ATT
GCT CAG CTG AAG TAC GGA TTA GAA GCC-3 0 and 5 0 -TGT
AGA AGA TCT ATT GTT CGG AGC AGT GCG GCG-3 0 .
Labeling of the DNA fragment was performed by phosphorylating the
5 0 -ends with [c-32P]ATP and T4 polynucleotide kinase. Before EMSA
analysis, the concentration of purified protein was first determined
using the modified Lowry reagent (Sigma) and was controlled by
fluorescence of EGFP in detail. Binding reactions containing 50 mM
Hepes, pH 7.5, 50 mM NaCl, 5 mM MgCl2, 20 lM ZnSO4, 10%
glycerol, and 2 lg/mL salmon sperm DNA were performed at 4 C for
20 min and at room temperature for 30 min based on the method
described elsewhere [15]. The protein–DNA complexes were resolved
on a 5% non-denaturing polyacrylamide gel containing 0.5· triborate
(TB) at 150 V for 3 h, and visualized with Typhoon 8600 image
analyzer.
Protein microarray fabrication. Fusion proteins of GAL4 DBD and
EGFP which were prepared in the binding buffer without any modifications were spotted onto the DNA immobilized glass surface of the
PCR product using spotting robotics. After 1 h, the slides were rinsed
with the binding buffer and blocked with BSA (2%w/v) in the binding
buffer for 1 h. EGFP protein was also prepared and treated in the
DNA immobilized glass as a negative control. To remove non-specific
bound proteins, the slides were intensively washed in a washing buffer
(20 mM Hepes, pH 7.5, 150 mM NaCl, 5 mM MgCl2, 20 lM ZnSO4,
0.05% Tween 20, and 20% glycerol).
GFP monoclonal antibody labeling and protein interaction analysis.
The monoclonal antibody for the interaction of EGFP on chip was
purchased (Clontech) and labeled with the fluorescent dye Alexa
Fluor 647 (Molecular probe). Labeling and purification of the protein
were carried out by the manufacturerÕs instruction (Molecular probe),
and molar concentration for labeled protein was calculated and
corrected for the absorbance of the dye at 280 nm. The labeled
antibody was dissolved in the binding buffer, and the protein-immobilized slides were incubated with the labeled antibody solution
for 1 h and washed violently by the washing buffer. The slides were
then scanned using the GenePix 4000B scanner (Axon Instruments).
PMT gain and power were set 600% and 100%, and analysis of
intensity was evaluated by the GenePixPro image analysis software
(Axon Instruments) to compare the fluorescent strength of the
proteins.
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was also overexpressed at 37 C, 0.4 mM IPTG, and
4 h induction, and purified by affinity chromatography.
When final purity of the protein was assessed by SDS–
PAGE, approximately more than 85% homogeneity
was obtained (Fig. 1B).
PCR product of UASG was prepared using no modified primers for the identification of binding affinity before DNA attachment of silylated glass surface. The
156-bp amplified DNA fragment included four binding
sites of GAL4 DBD such as 5 0 -CGG ATT AGA AGC
CGC CG-3 0 , 5 0 -CGG GTG ACA GCC CTC CG-3 0 ,
5 0 -AGG AAG ACT CTC CTC CG-3 0 , and 5 0 -CGC
GCC GCA CTG CTC CG-3 0 (Fig. 2A). It has been reported that the DNA sequence binds to the GAL4 DNA
binding domain with high affinity, although four binding sites have slightly different affinity, and has been
extensively used as binding sequence of yeast two-hybrid
system [15–17]. Titration of binding reaction of increasing amounts of the fusion protein (GAL4 DBD/EGFP)
with 20 fmol/lL DNA fragment was conducted (Fig.
2B). Because binding sites are closely spaced to one another, separated by only two nucleotides in case of three
sites, the binding affinity could not be quantitatively
determined. However, the purified protein was found
to bind as efficiently to the UASG as did GAL4 present
in other papers [15,18]. These preparations were useful
for most experiments described in this paper.
Protein microarray preparation
The approach used in this work to generate a DNA
surface appropriate for protein microarray, which was
possible in high-throughput fashion and oriented immobilization, was to prepare a double-stranded DNA sur-
Results and discussion
Protein purification and binding activity with DNA
To enable efficient production of the fusion protein,
the expression optimization was conducted with a variety of temperatures, IPTG concentrations, and induction times (data not shown). The fusion protein was
overexpressed at 20 C, 0.8 mM IPTG, and 20 h induction, and purified by affinity purification by Ni–NTA
agarose resin. And EGFP protein as a negative control
Fig. 2. The 156-bp PCR fragment of UASG and binding of GAL4
DBD/EGFP fusion protein with UASG. (A) The amplified fragment
included four binding sites (capital letter) of GAL4 DBD. (B) The
fusion protein complex was resolved by electrophoresis on 5% native
polyacrylamide gels. Binding reactions contained GAL4 DBD/EGFP
fusion proteins (10 nM, lane 1; 20 nM, lane 2; 40 nM, lane 3; and
80 nM, lane 4).
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Fig. 4. Antibody detection in the protein microarray.
Fig. 3. Fluorescence of the spots at various concentrations of GAL4
DBD/EGFP fusion protein immobilized on the microarray.
face to bind to the arrayed proteins with high binding
affinity. In addition, because proteins for microarray
were genetically modified, and these approaches provide
two advantages over chemical approaches such as controlled immobilization from a desired location and
unlimited production of modified protein. First, double-stranded DNA surface was prepared. For PCR
products shorter than 200-bp, the 5 0 -amine attached to
the PCR fragments has a clear effect of enhancing
cross-linking to silylated slides [19]. In this manner, the
156-bp DNA fragment amplified by 5 0 -amino modified
primers was attached on the silylated slides, and the
GAL4 DBD/EGFP fusion protein was then spotted
on the surface. The image of the microarray spotted
with a series of different fusion protein concentrations
is shown in Fig. 3, indicating that the spots printed as
low as concentration of approximately 60 lg/mL can
be detected. However, considering that EGFP optimum
excitation wavelength is 488 nm and the detection was
conducted by GenePix 4000B scanner with 532 nm laser,
much less amount of proteins can be detected by this approach. In addition, fluorescence intensity of spots at
the same concentration was more or less different, as described by the error bar. Because the performance of
covalent attachment of DNA into functionalized surfaces to yield stable and robust DNA layers of high
quality and reproducibility was first assessed as a function of probe DNA printing and attachment buffer solution [20], further optimization would be required to
obtain high quality image data in terms of probe spot
morphology, homogeneity, etc.
Protein–protein interaction
Monoclonal antibody of EGFP protein was used to
identify the immobilized protein on the surface. Fifty
micrograms per milliliter of antibody was labeled with
the fluorescent dye Alexa Fluor 647 reactive dye, and
was prepared in the binding buffer for the model experiment of protein–protein interaction. 400 lg/mL of
GAL4 DBD/EGFP fusion protein was spotted on the
slides. The protein-immobilized slides were incubated
with the labeled antibody solution for 1 h at room temperature, and the slides were also analyzed using the
GenePix 4000B scanner (Fig. 4). This result showed that
the conventional DNA surface was used to make a protein microarray directly and this approach was applied
to identify protein–protein interaction. Even though
we only looked at a model protein and the antibody,
the results present the fact that this approach is possible
to simply fabricate protein microarray using DNA surface directly in high-throughput fashion.
Fusion protein stability
The chip reproducibility and stability are very important to validate the feasibility of detecting specific interaction. In our approach, key consideration is that the
GAL4 DBD binding affinity with the binding DNA sequence should be conserved during protein microarray
analysis for reproducible and stable protein microarray
preparation. In this aspect, binding stability of the protein with DNA is very important, and the stability was
therefore investigated. After the protein purification,
the protein was incubated at 25 C with a series of times,
and the residual binding affinity was compared using
titration of EMSA (Fig. 5). The binding affinity was
approximately 2-fold decreased after 1 day, and the result indicated that the protein surface could not be conserved continuously. Although the protein–DNA
complex was constructed directly within 1 h and this
would not be critical for protein microarray fabrication
and analysis, much stable binding motif would be required to increase the reproducibility of the microarray.
And directed evolution and other related screening tools
such as cell surface display and phage display would give
Y.S. Choi et al. / Biochemical and Biophysical Research Communications 329 (2005) 1315–1319
Fig. 5. Residual binding activity of the GAL4 DBD/EGFP fusion
protein with the binding probe. The binding stability was measured by
estimating the residual binding activity by incubating the fusion
protein. (A) The protein–DNA complex at time 0 h, (B) the protein–
DNA complex at 1 day after purification, and (C) the protein–DNA
complex at 2 day after purification (160 nM protein, lane 1; 80 nM
protein, lane 2; and 40 nM protein, lane 3).
a solution by screening of DNA binding mutants with
high stable affinity [21–23].
In conclusion, a protein microarray is described
which addresses the challenge of a protein microarray
technology based on DNA chip platform, oriented protein immobilization, and high-throughput fashion by genetic modification of target protein. The results present
the fact that this approach has high potential for the
addition of the repertoire of protein microarray technologies for proteomics and focused protein profiling.
However, the stability of DNA binding domain would
need to be considered for the application of proteomics
and protein profiling by this approach.
Acknowledgment
This work was supported by Grant No. R01-2003000-10261-0 from the Basic Research Program of the
Korea Science and Engineering Foundation.
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