Howard Hughes Medical Institute, Department
of Molecular Biology and Genetics and Department of Neuroscience, Johns
Hopkins University School of Medicine, Baltimore, Maryland 21205
Received 4 March 1998/Returned for modification 27 May
1998/Accepted 5 August 1998
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INTRODUCTION |
Gene expression is temporally and
spatially regulated in a complex and organized sequence. Higher-order
complex formation requires the interplay between specific DNA sequences
and DNA-binding transcription factors, as well as additional components
that interact with the DNA-protein complexes through protein-protein
interaction. Certain structural elements, such as zinc finger motifs of
the transcription factor IIIA (TFIIIA) type (4, 25), the
basic helix-loop-helix motifs (27), basic leucine zippers
(b-zip) (39, 40) and POU/homeodomains (20, 33),
are shared by DNA-binding proteins and serve as an interface for DNA
recognition. Many of these proteins function in embryonic development
and regulate cell proliferation and differentiation. On the other hand,
leucine zipper motifs (22), helix-loop-helix domains
(1), LIM/double zinc finger domains (13), and PAS
domains (21) are implicated in mediating protein-protein
interactions that are essential for the function of those transcription
factors.
Roaz (rat Olf-1/EBF-associated zinc finger protein) is a 134-kDa
protein containing 29 C2H2 zinc finger domains
of the TFIIIA type (Fig. 1). The
C-terminal half of Roaz (RoazD86), containing 17 zinc finger
structures, was identified by its ability to associate with Olf-1/EBF
in a yeast two-hybrid screen and subsequently shown to display specific
interactions by biochemical assay and in cell line-based expression
systems (38). Further studies demonstrated that Roaz
functioned as a coregulator of Olf-1/EBF proteins to control olfactory
gene expression. Roaz abolished Olf-1/EBF-mediated transactivation of
the native promoters upstream of the olfactory marker protein (OMP) and
type III adenylyl cyclase (ACIII) by sequestering Olf-1/EBF proteins in
a heteromultimeric complex which failed to bind the Olf-1/EBF-binding
site. Expression of Roaz mRNA in adult mice was restricted to the lower
one-third of the olfactory epithelium consisting of basal cells,
neuronal precursors, and immature neurons. Notably, OMP and other
mature neuronal markers regulated by Olf-1/EBF proteins were expressed in the middle and upper regions of the epithelium in a complementary manner to Roaz. This pattern of expression, in conjunction with its
biochemical properties, suggested that Roaz acts as a switch protein
that contributes to the control of transition between the proliferative
and differentiated states.

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FIG. 1.
Schematic diagram and sequence comparison of the 29 zinc
fingers of Roaz. A schematic diagram of Roaz with individual zinc
finger structures represented by shaded boxes is depicted at the top.
The amino acid alignment of the 29 zinc fingers of Roaz is shown below.
The zinc-coordinating Cys and His residues are shown in bold letters,
and the conserved aromatic amino acids and branched aliphatic amino
acids are underlined. ZF, zinc finger.
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In contrast to the negative regulation at Olf-1/EBF-binding sites,
coexpression of Roaz and Olf-1/EBF proteins in a cell line-based transactivational assay led to a dramatic activation of reporter expression at a simian virus 40 (SV40) minimal promoter which lacked
Olf-1/EBF-binding sites. Further experiments revealed that Roaz protein
displayed direct binding to a specific region of this promoter
containing the six consecutive SP1 sites (38). In this
study, we identified a novel DNA sequence recognized specifically by
Roaz protein with high affinity through an in vitro binding-site selection assay (Selex) and characterized the protein structures involved in homomeric and heteromeric protein-protein interaction and
DNA-protein interaction. We showed that distinct TFIIIA zinc finger
motifs can mediate protein-protein or DNA-protein interaction and that
high-affinity DNA-protein association requires the presence of two
consensus half sites arranged in a palindromic sequence.
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MATERIALS AND METHODS |
Plasmid constructs.
pCIS-GSTRoaz was constructed by
subcloning a 4.5-kb EcoRV-NotI fragment isolated
from pBS-Roaz into the pCMV-GST expression vector (38).
pBS-Roaz was the composite cDNA clone reconstituted from three
different cDNA clones by using PmlI and BspEI
conserved sites between JBOZ2.1 and JBOZ1.3 and between JBOZ1.3 and
RoazD86 (38). pCIS-XPRoazD86 and pCIS-XPIC2 plasmid
constructs contain the RoazD86 and IC2 inserts (an irrelevant
polypeptide), respectively, tagged with an XPress sequence (DLYDDDDK;
Invitrogen, San Diego, Calif.); pCIS-GSTRoazD86 contained the RoazD86
insert fused with glutathione S-transferase (GST) in
pCMV-GST. pPC97-RoazD86 and pPC86-RoazD86 contain the RoazD86 inserts
cloned in the yeast expression vectors containing the GAL4 DNA-binding
domain (pPC97) or GAL4 transactivator domain (pPC86) (5).
Terminal truncation constructs were made with the Erase-a-base kit
(Promega, Madison, Wis.). N-terminal deletions of pPC86-RoazD86 were
made by protecting the SalI site and deleting from the
BspEI site. C-terminal deletions of pPC86-RoazD86 were made
by protecting the SpeI site and deleting from the
HpaI site. All deletion constructs were verified by DNA
sequence analysis.
Internal truncations of pPC86-RoazD86 and "broken-finger" mutants
were generated by single-stranded DNA mutagenesis. Single-stranded DNA
of pCIS-GSTRoazD86 was prepared by cotransfecting CJ236 cells with the
plasmid construct and helper phage and annealed with phosphorylated
mutagenic oligonucleotides. Extension and ligation reactions were
carried out at 37°C for 2 h in the presence of T4 DNA polymerase
and T4 DNA ligase. Double-stranded DNA was transformed into HB101
cells. Deletion mutants were first screened by PCR and later confirmed
by sequence analysis. The SalI-NotI fragments from individual mutant constructs were subcloned into the yeast expression vector (pPC86) for the yeast two-hybrid interaction assay.
The sequences of the mutagenic oligonucleotides are as follows: ind262,
5'-GCGTGAGCCATCGTCCTC|CTCGTTGCTGTGCTTCAC-3'; ind263,
5'-CAGCTGAGCTGCCAGCCAG|TCCGGGCCGGATGTTATG-3'; ind264, 5'-ACACTCATGGTTGATGCC|CTTCTGCATGTGAAAGGTG-3'; bzf275,
5'-GTTCGATGAGGTTACAAAGGAGC-3'; and bzf277,
5'-GCTCATCGTGTTGTTCTGCAAC-3'. Vertical lines in
the internal deletion constructs indicate the deletion sites; the mutated nucleotides in the "broken-finger" mutants are underlined.
EMSA.
An electrophoretic mobility shift assay (EMSA) was
carried out essentially as described previously (15, 41)
with the following modifications. Protein was mixed with specified
amounts of probe in a 20-µl binding-reaction mixture and incubated at
20°C for 20 min. The binding-reaction mixture contained 10 mM HEPES
(pH7.9), 70 mM KCl, 1 mM dithiothreitol, 4% glycerol, 2.5 mM
MgCl2, 100 µM ZnCl2, 1 mM EDTA, 100 µg of
poly(dI-dC) per ml, and 20 µg of salmon sperm DNA per ml unless
indicated otherwise. The mixture was subjected to electrophoresis on
either a 6% polyacrylamide gel (acrylamide/bisacrylamide ratio, 59:1)
or a 1.5% agarose gel (SeaKem, Rockland, Maine) in 0.25×
Tris-borate-EDTA (TBE) at 4°C. The products were detected by
autoradiography of the dried gel.
For the Selex assay and DNA-binding affinity study, PCR products were
labeled with [
-32P]ATP by using T4 DNA polynucleotide
kinase in a 20-µl reaction mixture. For the DNA-binding assay of
C-terminal truncation, complementary oligonucleotides with a 5' GATC
overhang were annealed in annealing buffer (100 mM KCl, 10 mM Tris [pH
8.0], 1 mM EDTA) at 100°C for 5 min and 68°C for 1 h, and
slowly cooled to room temperature. Double-stranded DNA fragments were
gel purified, and 75-ng portions of the isolates were labeled with
[
-32P]dCTP by using the Klenow fill-in reaction.
Selex.
Optimal DNA sequences for Roaz binding were
determined by a PCR-amplified Selex protocol (42, 43). The
76-mer oligonucleotides (5'-CATGAAT TCTCCTATACTGAGT TCATGATN18TGATATCGAACTGTATCGATGAAT TCCAC-3')
including 18 random nucleotides and two PCR primer sequences corresponding to the first (top strand) 20 bases and complementary to
the last (bottom) 20 bases were chemically synthesized. A random sequence library was generated by a primer extension reaction carried
out with the purified 76-mers as template and the bottom-strand primer
in a 20-µl Klenow reaction mixture. Double-stranded DNA fragments
were gel purified on a 4% low-melting-point agarose gel and labeled
with [
-32P]ATP by using T4 DNA polynucleotide kinase.
Radiolabeled probes (3 × 104 cpm) were mixed with 60 ng of GST-Roaz fusion protein purified through a GST affinity column
(38) in EMSA with 20 µl of buffer. The gel was subjected
to autoradiography, and the regions corresponding to the shifted bands
were cut out and separately eluted in 250 µl of elution buffer (500 mM ammonium acetate, 1 mM EDTA [pH 8.0]) for 4 h at 37°C. A
fraction of the eluate (10 µl) was used for subsequent PCR
amplification with 10 ng of each primer per µl and 0.2 mM each
deoxynucleoside triphosphate in a 50-µl reaction mixture. PCR was
programmed as 50°C for 1 min, 72°C for 1 min, and 94°C for
30 s for 35 cycles. The PCR products were then gel purified,
radiolabeled, and subjected to the next round of EMSA. Nine rounds of
EMSA selection were performed, with PCR amplification after each round.
The final products were digested with EcoRI, subcloned into
pBlueScript, and analyzed by sequence analysis with T7 primer.
Measurement of the apparent dissociation constant.
The
apparent dissociation constant (Kd) of Roaz
binding to specific DNA fragments was estimated as the protein
concentration at which half of the DNA probe was shifted in an EMSA.
Probes were prepared from purified PCR fragments containing different inserts and radiolabeled with [
-32P]ATP in a kinase
reaction. For affinity studies, individual probes (2 pM) were mixed
with purified GST-Roaz full-length protein at 1, 2, 4, 8, 16, and 32 nM
in the presence of 100 µg of dI-dC per ml and 20 µg of salmon sperm
DNA per ml and incubated at room temperature for 30 min to reach
equilibrium (11). The intensity of shifted bands was
measured with a PhosphorImager (Molecular Dynamics, Sunnyvale, Calif.).
Affinity chromatography and zinc removal experiment.
RoazD86
or OED5 (a partial sequence of Olf-1/EBF isolated from the original
yeast two-hybrid screen [38]) was expressed as a GST
fusion protein by transient transfection into HEK-293 cells. Four
100-mm-diameter plates of HEK-293 cells were collected, washed twice
with 1× phosphate-buffered saline (PBS), and extracted with 4 ml of
extraction buffer (1× PBS, 1% Triton, 1 mM phenylmethylsulfonyl fluoride, 1 µg of leupeptin per ml, 2 µg of aprotinin per ml, 1 µg of pepstatin A per ml) for 30 min at 4°C. After the extract was
precleared by centrifugation at 15,600 × g for 20 min,
300 µl of a 50% slurry of glutathione-bound agarose beads was added to the supernatant and mixed at 4°C for 1 h. The beads were
washed once with 1× PBS, once with 1× PBS plus 500 mM NaCl, and three times with 1× PBS. Whole-cell extracts were isolated from HEK-293 cells transfected with pCIS-XPRoazD86 and mixed with GST fusion protein
bound to glutathione-agarose beads. After a 2-h mixing at 4°C, the
beads were washed once with 1× PBS, twice with 1× PBS plus 500 mM
NaCl, and three times with 1× PBS. Sample buffer was added, and a
fraction was resolved by sodium dodecyl sulfate-polyacrylamide gel
electrophoresis (SDS-PAGE) (10% acrylamide). In the zinc removal experiment, whole-cell extract was treated with 1 mM EDTA, 5 mM EDTA,
or 1 mM 1,10-phenanthroline and mixed with GST-RoazD86 or GST-OED5
bound to glutathione-agarose beads for the in vitro binding assay. All
in vitro binding experiments were carried out essentially as described
above unless indicated otherwise in the figure legends.
In vitro transcription-translation of C-terminal truncations of
Roaz and Roaz(bzf277).
In vitro transcription-translation was
carried out with a TNT-coupled wheat germ extract system (Promega). The
pBS-XPRoaz vector was generated in two steps. First, a 4.5-kb
KpnI-NotI fragment from pBSRoaz was subcloned
into pEBVHisC (Invitrogen). A 4.9-kb EcoRI-XbaI
fragment, containing an in-frame ATG with Kozak consensus sequence, six
histidine residues, and an XPress tag at the 5' end, was isolated and
subcloned into pBlueScript vector. pBS-XPRoaz was digested individually
with BsgI, HaeII, PmlI,
BspEI, and NotI to generate C-terminal
truncations (CD1, CD2, CD3, and CD4) and full-length protein,
respectively. pBS-XPRoaz(bzf277), encoding a full-length Roaz as
described above except for a "broken" 29th finger, was constructed
by inserting a BspEI-NotI fragment from pCIS-GSTbzf277 into pBS-XPRoaz. These linearized DNA fragments (2 µg)
were used for in vitro transcription-translation with unlabeled methionine as described by the manufacturer.
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RESULTS |
In vitro selection of the Roaz-binding site.
The ability of
Roaz to activate the expression of an SV40 early promoter-regulated
reporter gene in the presence of Olf-1/EBF proteins suggested that the
Roaz-Olf-1-EBF heterocomplex encoded specific DNA-binding activity.
An EMSA with purified Roaz and Olf-1-EBF indicated that the DNA
recognition ability of the Roaz-Olf-1-EBF heterocomplex was likely to
be conferred by the Roaz protein, and the target sequence was mapped to
a region composed mainly of six consecutive SP1 sites (38).
To address the DNA-binding specificity in general and to identify other
possible binding sequences, we used a Selex protocol (see Materials and
Methods) (42, 43) in which a glutathione-Sepharose-purified GST-Roaz fusion protein (60 ng, 16 nM) was used to select for optimal
binding sequences from a DNA library containing a pool of random
18-mers flanked by PCR primer sequences. Shifted DNA-protein complexes
of three different mobilities were observed after the first round of
selection, with the top and middle bands showing the highest
intensities. Two independent Selex procedures were performed
individually to select for bound DNA sequences corresponding to either
the top or middle band. Eight subsequent rounds of EMSA selection were
carried out with purified GST-Roaz fusion protein (60 ng or 16 nM for
the first three rounds, and 30 ng or 8 nM for the last five rounds) and
radiolabeled PCR products (30,000 cpm) from the previous round of
selection.
DNA sequence analysis of 20 isolates from the final round of Selex for
the top complex and 14 isolates from the Selex for the middle complex
revealed a consensus sequence composed of a perfect or imperfect
palindromic sequence [GCACCC(A/ T)(A/T)GGGTGC] in
every sequence examined (Fig. 2). The
inferred consensus sequence contained a match to the consensus half
site GCACCC, a spacer of 2 nucleotides (A or T in either
position), and an inverted half site (GGGTGC) or an
imperfect inverted half site with a single nucleotide substitution at
one of the last two positions (GGGTGA, GGGTGT, GGGTCC). To
confirm that the starting library was generated randomly, 25 clones of
the original library were sequenced and the average frequency of
different nucleotides in each position was estimated to be 24, 28, 24, and 24% for G, A, T, and C, respectively. None of these clones
contained a single half site (GCACCC or GGGTGC). The probe derived from the top band or the middle band in each step of the Selex procedure resulted in an increased intensity of all
three complexes in the next round of EMSA (data not shown). These
observations suggest that these three bands contain similar DNA
sequences and are likely to represent monomeric and multimeric complexes of Roaz.

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FIG. 2.
Roaz-binding sites from the Selex assay. Sequence
alignment of 34 isolates from the final round of PCR amplification is
shown. The top 6 sequences were derived from 20 isolates from Selex for
the top band; the bottom eight sequences were derived from 14 isolates
for the middle band. The conserved sequences are underlined, and the
two palindromic repeats are shown in bold letters. In six of the
sequences, part of the consensus is contributed by the adjacent primer
sequence (parentheses). The number of appearance is given in the right
column. Italics indicate non-consensus primer sequence.
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Roaz binds a canonical sequence with an apparent
Kd of 3 nM.
The DNA-binding affinity of
Roaz protein was assessed by the protein concentration required to
shift half of the DNA probe in an EMSA. In this equilibrium study, less
than 2 pM radiolabeled DNA probe was mixed with purified GST-Roaz
protein at 1, 2, 4, 8, 16, and 32 nM for 30 min at room temperature,
and DNA-protein complexes were resolved on a 1.5% agarose gel. The
protein concentration at which half of the DNA probe was shifted was
designated the apparent dissociation constant
(Kd). The Kd for GST-Roaz
binding to the complex DNA probes from the last round of Selex for
either the middle or top band was estimated to be around 8 nM (Fig.
3A). The Kd for a
canonical palindromic sequence, 9H5 (Fig. 2), was measured in a similar
experiment and estimated to be 3 nM (Fig. 3B). To distinguish the
orientation and spacing effect from a dosage effect of binding sites,
two half sites (GCACCC) were created on a single probe
separated by 13 nucleotides and arranged in direct-repeat orientation.
The Kd for this probe (X2SX) was estimated to be
over 16 nM (Fig. 3C), five- to sixfold higher than that for the
inverted repeat.

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FIG. 3.
DNA-binding affinity study. (A) A mixture of complex
probes (2 pM) from the Selex for the middle band (left) or top band
(right) was mixed with purified GST-Roaz, at increasing concentrations
as indicated, in the EMSA. (B and C). Parallel experiments to that in
panel A, except that a canonical palindromic repeat (9H5) or a direct
repeat with 13 bp (X2SX,
GCACCCATCGTCGAGATTAGCACCC) was used as
a probe in the EMSA, respectively.
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Structural analyses of homodimerization and heterodimerization by
Roaz.
The selection of a large number of independent clones with
inverted repeats by Selex (Fig. 2) and the existence of
slower-migrating species in the EMSA (Fig. 3) suggested that Roaz might
bind DNA as multimeric complexes. The physical interaction was
shown by an in vitro binding assay (Fig.
4A). RoazD86 tagged with XPress epitope
(XP-RoazD86) could be specifically retained on
glutathione-coupled Sepharose beads containing GST-RoazD86 (lane 1) but
not on beads containing GST (lane 2). The specificity was confirmed by
mixing XPIC2 (an irrelevant polypeptide tagged with XPress epitope)
with GST-RoazD86 (lane 3) in a similar experiment.

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FIG. 4.
Biochemical characterization of the Roaz protein-protein
interaction. (A). Purified proteins (6 to 8 µg of GST or GST-RoazD86
fusion protein bound to 20 µl of a 50% slurry of glutathione-agarose
beads) were mixed with whole-cell proteins (400 µg) isolated from
HEK293 cells transfected with pCIS, pCIS-XPIC2, or pCIS-XPRoazD86.
Bound proteins were extracted with 25 µl of sample buffer, and a
portion (8 µl) was fractionated by SDS-PAGE (10% polyacrylamide) and
detected by Western blotting with anti-XPress antibody (Invitrogen). A
1/25 portion of the input sample was loaded for comparison. (B) GST
fusions of RoazD86 (2 µg) (left) or OED5 (3 µg) (right) were mixed
with whole-cell extract (300 µg) isolated from HEK-293 cells
transfected with pCIS-XPRoazD86 pretreated with 1 mM EDTA (lane 2), 5 mM EDTA (lane 3), or 1 mM 1,10-phenanthroline (lane 4) for the in vitro
binding assay. Half of the bound protein was fractionated by SDS-PAGE
(10% acrylamide). A 1/40 portion of the input sample was loaded in
lane 5 for comparison.
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The only discernible structural motifs present in RoazD86 were 17 C2H2 zinc fingers distributed along 700 amino
acids. To examine the possible roles of these zinc finger motifs
in mediating the protein-protein interaction, we performed a
zinc removal experiment by treating the XPRoazD86-containing
extracts with 1 or 5 mM EDTA to remove divalent cations or with 1 mM 1,10-phenanthroline (a zinc chelator). GST-RoazD86 (2 µg) or
GST-OED5 (3 µg) was subsequently added to the EDTA- or
1,10-phenanthroline-treated protein extract in a binding assay
(Fig. 4B). OED5 encoded residues 221 to 570 of Olf-1-EBF, which were
sufficient for Roaz-Olf-1-EBF heterocomplex formation
(38). Roaz-Roaz homodimerization (Fig. 4B, left) and Roaz-Olf-1-EBF heterodimerization (right) were both abolished in the
presence of EDTA (lanes 2 and 3), or 1 mM 1,10-phenanthroline (lanes
4). The 70-kDa band (Fig. 4B, right) represented the GST-OED5 protein
that could cross-react with the anti-XPress antiserum. Coomassie blue
staining showed that the binding of GST-RoazD86 and GST-OED5 to
glutathione-coupled agarose beads was not affected by the 1 mM
1,10-phenanthroline or 5 mM EDTA treatment (data not shown).
The regions of Roaz involved in homomultimerization and specific
intermolecular interactions with Olf-1-EBF were identified in the
yeast two-hybrid interaction assay with a series of N-terminal-, C-terminal- and internal-deletion constructs of RoazD86 fusion protein
with the Gal4 transactivator domain (Gal4TA-RoazD86). The strength of
interaction was determined by a
-galactosidase assay in yeast liquid
cultures (2) and expressed as a percentage of the activity
observed for interactions of the intact Gal4TA-RoazD86 with the
Olf-1-EBF or RoazD86 proteins fused to the Gal4 DNA-binding domain
(Fig. 5A). The relative
level of protein expression for each construct was assessed by Western
blotting with an anti-Gal4TA antibody and found to vary less than
twofold, except for bzf277, which was expressed at one-third the level
of the intact protein, and nnd20, which was expressed at less
than one-third the level (unpublished data). The
deletions of RoazD86 revealed that a region corresponding to the last
85 amino acids (amino acids 1102 to 1186) and encoding the last three
zinc finger motifs was essential for Roaz-Olf-1-EBF
heterodimerization. Loss of this region resulted in a 17-fold reduction
in the protein-protein interaction. All constructs which removed this
region (cnd20, cnd13, cnd13.2, and cnd12.2) resulted in a dramatic
reduction in the Roaz-Olf-1-EBF interaction. Internal deletions of
about 150 amino acids across the protein coding region led to
activities similar to (ind264) or modestly reduced from (ind262 and
ind263) that of the intact protein. The low activity observed in the
nnd20 construct can be accounted for by the reduced protein expression
level. When the homomultimeric interaction of Roaz with itself was
examined with the same set of constructs, normal levels of activity
were seen in all cases, with the exception of cnd12.2, where the
interaction was reduced 20-fold.

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FIG. 5.
Regions essential for hetero- and
homomultimerization of Roaz. (A). Yeast strain Y190, harboring the GAL4
DNA-binding domain fusions to Olf-1-EBF or RoazD86, was transformed
with constructs encoding C-terminal deletions (cnd), N-terminal
deletions (nnd), internal deletions (ind), or broken-finger mutants
(bzf) of RoazD86 as GAL4 transactivator domain fusions. Double
transformants were assayed for -galactosidase activity. The
positions of the amino acids (aa) which define the deletions in the
nnd, cnd, and ind constructs and the zinc finger which is mutated in
the bzf constructs are indicated in parentheses. The strength of
interaction for an individual mutant is expressed as a percentage
relative to that of intact proteins, which is set at 100% and
corresponds to 43 ± 7 U for Roaz-Olf-1-EBF and 26 ± 5 U
for Roaz-Roaz interactions. All measurements were determined for at
least four independent colonies. A schematic diagram of
Gal(TA)-RoazD86, with each shaded box representing a zinc finger
structure, is shown at the top. Numbers under the boxes refer to the
positions of the fingers. Mutated zinc fingers in the bzf constructs
are indicated by solid ovals. Zf, zinc finger. (B) Biochemical
characterization of heterodimerization between Roaz mutants and
Olf-1-EBF. Whole-cell extracts (100 µg) from HEK-293 cells
transfected with pCIS-Olf-1-EBF were mixed with 50 ng of individual
GST or GST fusions bound to Sepharose beads as indicated. Half of the
retained proteins and 2.8 µg of input whole-cell extracts were
resolved by SDS-PAGE and Western blotted with either anti-Olf-1-EBF
antiserum (left) or anti-GST antiserum (right). (C) Biochemical
characterization of homodimerization with Roaz mutants. Whole-cell
extracts (400 µg) from HEK-293 cells transfected with pCIS-XPRoazD86
were mixed with 4 µg of individual GST or GST fusions bound to
Sepharose beads as indicated. One-third of the retained proteins and 10 µg of input whole-cell extracts were resolved by SDS-PAGE (10%
polyacrylamide) and Western blotted with either anti-XPress antiserum
(left) or anti-GST antiserum (right). Solid circles indicate the
positions of aggregates of GST multimers, and asterisks indicate
proteolytic products.
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To definitely demonstrate that specific Zn fingers mediate
protein-protein interactions, a set of "broken-finger" mutations with histidine-to-asparagine substitutions at the third zinc ligand position (10) was generated at the 27th (bzf275) or 29th
(bzf277) zinc finger in a region crucial for heteromultimerization with Olf-1-EBF (Fig. 5A). The strength of the protein-protein interaction was assessed as described above. Roaz with a broken 29th finger preferentially affected its ability to bind Olf-1-EBF (3%) while producing only a modest reduction in interaction with itself (36%). In
light of the threefold reduction of fusion protein expression observed
with this construct, we inferred that the last finger is specifically
involved in Roaz-Olf-1-EBF interaction. In contrast, a broken 27th
zinc finger displayed normal interaction with both Olf-1-EBF and Roaz.
The regions of Roaz involved in homo- and heterodimerization were
further corroborated by in vitro binding experiments. Three constructs,
RoazD86, bzf277, and cnd20 (Fig. 5A), were expressed as GST fusions and
assayed for their ability to heterodimerize with Olf-1-EBF. A
broken-finger mutation, bzf277, resulted in a significant
reduction in the amount of the retained Olf-1-EBF protein (Fig.
5B, left, lane 3) compared with RoazD86 (lane 2), whereas a
C-terminal truncation of 85 amino acids (cnd20) exhibited no detectable
binding to Olf-1-EBF (lane 4) under these conditions. The use of an
anti-GST antibody on a parallel blot (Fig. 5B, right) demonstrated that
comparable amounts of the GST fusions were present on the resins used
in each sample. The regions of RoazD86 essential for
homodimerization were examined in a similar fashion by using RoazD86, bzf277, cnd20, cnd13-2, and cnd12-2 (Fig. 5C). The results confirmed that cnd12-2 had lost most of its ability to interact with
RoazD86 (Fig. 5C, left, lane 6), consistent with the observations in
the yeast two-hybrid interaction assay. Control experiments for the
amount of GST fusions were performed in parallel as described above
(Fig. 5C, right). Native GST, a negative control, failed to interact
with Olf-1-EBF or RoazD86.
DNA binding of Roaz to a single half site and inverted repeat
involves the first seven zinc finger motifs.
The higher binding
affinity of Roaz to the GCACCC inverted repeat than to the
direct repeat separated by 13 nucleotides (Fig. 3) and the ability of
full-length Roaz to associate with itself (Fig. 4A) suggested that
protein dimerization might play an important role in Roaz binding to
DNA. Furthermore, Roaz-binding sites identified from the Selex assay
with full-length Roaz protein had no affinity for RoazD86, the
C-terminal half of Roaz protein, suggesting that DNA binding required
the N-terminal half of Roaz (unpublished data). To define the
DNA-binding domain in Roaz and to dissect the cooperative binding of
the Roaz homodimer from the possible dosage effect, several
C-terminally truncated Roaz proteins (RoazCD1, RoazCD2, RoazCD3, and
RoazCD4) containing 1 (the first), 7, 8, and 13 zinc finger motifs,
respectively, were generated by restriction digestion of the
full-length Roaz cDNA and subsequent in vitro transcription-translation
(Fig. 6A). These truncated proteins lacked the C-terminal region essential for mediating homodimerization as well as heterodimerization in solution. Roaz(bzf277), encoding a
full-length protein with a broken 29th finger, demonstrated little
heterodimerization activity, while its ability to homodimerize remained
largely intact (Fig. 5). EMSA was performed with an equivalent amount
of individual proteins, normalized by measuring the incorporated 35S-labeled methionine, mixed with probes containing an
inverted repeat of consensus sites (X2.RBS,
GCACCCTTGGGTGC), a single
half site (X1.RBS, GCACCC), an inverted repeat with two
nucleotide substitutions in the consensus sequence (X2.MUT,
GAACTCTTGAGTTC), or a direct repeat of the consensus half site spaced by 13 nucleotides (X2SX) (Fig. 6B). Probes were designed so that the flanking
sequences in all probes and spacing sequence in the direct-repeat probe were the same (AGATTA at the 5' end, ATCGTC at
the 3' end).

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|
FIG. 6.
Characterization of DNA-binding domains in Roaz. (A)
Schematic diagram of C-terminally truncated Roaz proteins (CD1, CD2,
CD3, and CD4) and broken-finger mutant Roaz(bzf277). Numbers in
parentheses indicate the starting and ending amino acids (aa). (B) DNA
sequences of synthetic oligonucleotides containing a consensus half
site (X1.RBS), a consensus inverted repeat (X2.RBS), a mutated inverted
repeat (X2.MUT) and a direct repeat (X2SX). The consensus sequences
recognized by Roaz are indicated by bold letters. (C to E) EMSA with
32P-labeled probes as indicated and truncated forms of
recombinant Roaz, full-length protein, single broken-finger mutant
(bzf277), and control lysate (Ctrl) as shown in panel A. The positions
of dimeric and monomeric forms of recombinant proteins are indicated by
circles and asterisks, respectively. FP, free probe. (C and D) 6%
polyacrylamide gel. (E) 1.5% agarose gel.
|
|
Roaz proteins containing the N-terminal seven zinc finger
motifs [RoazCD2, RoazCD3, RoazCD4, Roaz, and
Roaz(bzf277)] formed complexes with the inverted repeat
(X2.RBS) substrate on a 6% polyacrylamide gel (Fig. 6C, left). Two
complexes with different mobilities were observed most clearly with
CD2, CD3 and CD4 proteins. The shifted complexes with higher
mobility consisted of monomer bound to a single half site, as suggested
by a parallel EMSA performed with the single half-site probe (X1.RBS)
labeled to the same specific activity (Fig. 6C, middle). With the
X1.RBS probe, only the complexes with higher mobility could be seen. In
contrast, complexes with lower mobility formed only on the inverted
repeat and presumably represented dimer formation on the palindromic
sequence. EMSA with full-length Roaz or Roaz(bzf277) showed only
dimeric binding on the inverted repeat and no monomeric binding on
either the inverted repeat or the single half site. The intensities of
the Roaz and Roaz(bzf277) dimers on the inverted repeat were lower than those of RoazCD2, RoazCD3, and RoazC4. One simple explanation was
that the majority of radioactivity for full-length Roaz and Roaz(bzf277) was retained in the wells on a 6% polyacrylamide gel
due to the size of the multimeric complexes (>260 kDa). To further
resolve the larger complexes, the same reaction was run on a 1.5%
agarose gel (Fig. 6E). The dimeric protein-DNA complexes of Roaz and
Roaz(bzf277) became the predominant species, although a significant
amount of radioactivity still remained in the wells.
The formation of dimers on the inverted repeat by RoazCD2, RoazCD3,
and RoazCD4 recombinant proteins which lack the essential dimerization
domain in solution suggests that two properly oriented and spaced half
sites may position these C-terminally truncated proteins in such a way
that they can bind cooperatively; alternatively, it may be due to a
simple dosage effect or double occupancy on the two half sites. To
differentiate these two possibilities, a direct repeat of GCACCC
spaced by 13 nucleotides was generated and used in a parallel
EMSA experiment (Fig. 6C, right). With the direct-repeat probe, only
Roaz and Roaz(bzf277) displayed dimer-DNA complexes whereas the
other constructs developed only monomeric binding. The specificity of
the consensus site in the EMSA was compared with that of a mutated
inverted repeat with the same flanking sequence and two base pair
changes in the consensus half site (X2.MUT; Fig. 6B). No shifted
DNA-protein complexes could be detected with any of the proteins (Fig.
6D).
 |
DISCUSSION |
Roaz binding-site selection.
To demonstrate the specific
DNA-binding ability of Roaz and also to identify the candidate target
sequences, we used the Selex method to show that Roaz recognizes a
novel perfect or imperfect inverted repeat of GCACCC in this
assay. The apparent Kd of Roaz to one canonical
palindromic sequence, 9H5, was approximately 3 nM. Since this number is
3 orders of magnitude higher than the amount of probe, it is likely to
represent the true dissociation constant (Kd) in
vitro. The presence of inactive protein generated during the
purification process or EMSA and binding of Roaz protein to
single-stranded DNA would make the actual Kd
even lower than what was measured. In this assay, we limited our
findings to sequences less than 18 nucleotides and of relatively high
affinity, two limitations intrinsic to the Selex protocol. As a result,
important sequences that require a larger neighboring context or are
regulated in a dynamic manner will not be identified. Nevertheless, the identification of the Roaz consensus binding sequence allowed us to
address its DNA binding mechanism and may provide an important clue to
illuminating gene expression controlled by Roaz in vivo. This is
particularly significant, given the difficulty and limitation of
approaches available for identifying downstream targets of specific
transcription factors.
Direct involvement of distinct zinc fingers in protein-protein
interaction.
The first zinc-requiring transcription factor, the 5S
rRNA gene-specific TFIIIA in Xenopus (17), bears
repeated motifs of two Cys and two His residues (4, 25). The
DNA-binding ability and crystal structure of
C2H2 zinc fingers is demonstrated by EMSA and
X-ray crystallography of single-finger or two-finger peptides
(28). In the study, each of the C2H2
zinc fingers represents a structurally and functionally independent
domain and contributes to the recognition of three consecutive
nucleotides in the major groove. A subsequent crystal structure study
of a five-finger GL1-DNA complex shows that different fingers can play
very different roles in DNA recognition (29). Chemical and
biochemical studies of TFIIIA also demonstrate the distinct roles of
different finger motifs (6, 7, 10, 18, 19, 32). For proteins
with a large number of consecutive zinc fingers, interpretation of the
structure and function of individual fingers can be even more problematic. For proteins like Roaz (29 fingers) and Xfin (37 fingers)
(34), the contribution of individual finger structures to
DNA binding remains largely unknown.
Recent work has revealed an additional role for
C2H2 zinc finger motifs in the protein-protein
interaction and higher-order complex formation. Such examples include
human immunodeficiency virus type 1 integrase (12), SV40
large T antigen (23), GATA-1/erythroid Kruppel-like factor
(14), TFIIIA (9), Aiolos/Ikaros (26, 37), YY1/CREB (44), serendipity-
(30),
and aspartate transcarbamoylase (24). Other
zinc-requiring transcription factors such as the nuclear receptor of
the four-Cys type (31), LIM/double-zinc-finger motifs
(13, 35), and modified zinc finger structure (36) have all been shown to participate in protein dimerization. In this
study, the direct involvement of zinc finger motifs of Roaz in
protein-protein interactions is shown by the zinc removal experiment and by use of a set of broken-finger mutants which abolish the individual zinc finger motif without perturbing the overall protein organization and length. One interesting aspect of Roaz is that the
region essential for the Roaz-Olf-1-EBF interaction (amino acids 1102 to 1186) is largely dispensable for Roaz-Roaz homodimerization. A
broken finger of the last zinc finger affects predominantly the
heterodimerization of Roaz with Olf-1-EBF while preserving its
homodimerization activity. In contrast, the lack of interaction of Roaz
with cnd12-2 but not with C-terminal truncations that extend to amino
acid 999 implies that this region (amino acids 947 to 999) is critical
for homomeric interaction. However, internal deletion of this region in
ind264 results in normal activity. These observations support a role
for individual fingers of Roaz in protein recognition specificity and
suggest some degree of redundancy in the regions required for homomeric
interactions.
Based on the observations presented in this paper, we conclude that the
zinc finger motif in Roaz can serve as an interface for protein-protein
interactions as well as playing well-established roles in DNA
recognition. An attractive corollary of this hypothesis is that
proteins possessing multiple zinc fingers such as Xfin and Roaz may
utilize some specific domains for protein-protein interaction, which is
important in mediating cooperative DNA binding and recruiting addition
cofactors with activational or inhibitory activity. The difference in
the functional specificity of individual fingers cannot be resolved at
the amino acid sequence level, since sequence comparison of the 29 zinc
fingers reveals that in addition to the Cys and His residues that
directly coordinate zinc ions, most of them contain a conserved
aromatic amino acid, F or Y, and a branched aliphatic amino acid (Fig.
1). Therefore, it is likely that residues which are not conserved in
all of the Zn fingers contribute to the distinct functions.
Mechanism of DNA binding by Roaz.
EMSA with a series of
C-terminally truncated Roaz protein mapped its DNA-binding domain to
the N-terminal seven zinc finger motifs, which display both monomeric
binding on a single half site and dimer binding on the inverted repeat.
The formation of dimers for CD2, CD3, and CD4 on the inverted repeat
but not on the single half site or direct repeat with a 13-bp spacer
reveals that DNA recognition of the inverted repeat is contributed by both partners in the homodimer, each interacting with a single half
site. Although the first seven zinc fingers fail to form a stable dimer
in the solution, they can mediate dimerization in the presence of
inverted repeat. A similar property is also described for DNA binding
of transcription factors including the N-terminal region of Olf-1-EBF
(16). On the other hand, full-length Roaz and
Roaz(bzf277) can mediate dimer formation on both the inverted
repeat and direct repeat. Under the conditions used, the low binding
affinity for monomer binding to a single half site would make a direct
repeat with double occupancy almost undetectable. This might explain
the lack of noncooperative binding of two monomers of the C-terminal
truncations to the direct repeat. These experiments suggest that a
majority of Roaz and Roaz(bzf277) assemble multimers in solution
and that multimeric-complex formation may interfere with their binding
to the single half site. Finally, Roaz(bzf277) demonstrates the
same DNA binding pattern as Roaz for all the probes tested. This
construct can potentially be used to study the specific function of
Roaz in transcriptional regulation.
Possible roles of Roaz-binding sites in vivo.
Roaz-binding
sites, GCACCC inverted repeats, identified through the Selex
assay are reminiscent of a group of GC-rich sequences recognized by a
subset of TFIIIA-type zinc finger protein which includes SP1,
Zif268/NGFI-A/ Krox-20,24/Egr1,2/Wilms' tumor family, and yeast ADR1
(3). Interestingly, the consensus half site bears a close
resemblance to the SP1 recognition sequence, CCGCCC, which has been shown to be able to confer
Roaz-Olf-1-EBF-mediated reporter activation in a cell-line-based
assay (38). To date, we have not been able to mimic this
activation by replacing the endogenous SP1 sites in the SV40 early
promoter with eight consecutive Roaz half-site (GCACCC)
repeats. The arrangements of the sites with respect to other
promoter elements may have precluded the activation of transcription
from this promoter. A second reporter construct consisting of the eight
repeats and a minimal thymidine kinase (TK) promoter was also used. The
high background activity of Olf-1-EBF transfection with the minimal TK
promoter prohibited us from examining the cotransfection of
Roaz-Olf-1-EBF with this reporter. Nevertheless, the lack of
activation of Roaz homomultimer on both reporter constructs may suggest
that Roaz lacks intrinsic transactivational activity.
A search for Roaz-binding sites in the available proximal promoter
region of several olfactory specific genes, including olfactory marker
protein (OMP) (8), Golf, type III cyclase
(ACIII) olfactory cyclic nucleotide-gated channel, 50.06, and 50.11 (41), reveals no identical sequences to the inverted repeat,
although a single half site is found in Golf (position
557) and ACIII (position
114), and a SP1 site in OMP (position
46) and Golf (position
252). Unfortunately, potential
target genes for Roaz homodimer or Roaz-Olf-1-EBF heterodimers in the
basal-cell population of the olfactory epithelium are unknown.
Characterization of the DNA-binding specificity may provide an avenue
to identify them.
In summary, Roaz represents a complex transregulatory molecule that
utilizes a structural motif, the C2H2 zinc
finger, to perform DNA binding and protein dimerization functions. Roaz
plays discrete roles in transcriptional regulation. When complexed with the Olf-1-EBF proteins, it inhibits transcriptional activation at the
Olf-1-EBF-binding site by sequestering the Olf-1-EBF proteins and
preventing the formation of an active DNA-binding Olf-1-EBF homodimer.
The heteromeric complex of Olf-1-EBF and Roaz possesses transactivational activity at distinct sites where DNA binding is
mediated by the Roaz protein (38). We describe here the
direct binding of Roaz to a consensus inverted repeat through the
N-terminal seven zinc finger motifs. In vivo, Roaz may activate or
repress transcriptional activity by recruiting additional repressor or coactivator through the C-terminal dimerization domain.
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