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Molecular and Cellular Biology, July 1999, p. 4711-4718, Vol. 19, No. 7
0270-7306/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.
Major Egr3 Isoforms Are Generated via Alternate
Translation Start Sites and Differ in Their Abilities To
Activate Transcription
Kevin J.
O'Donovan and
Jay M.
Baraban*
Departments of Neuroscience and Psychiatry
and Behavioral Sciences, Johns Hopkins University School of
Medicine, Baltimore, Maryland
Received 9 December 1998/Returned for modification 10 February
1999/Accepted 6 April 1999
 |
ABSTRACT |
In previous studies, we detected a major, unidentified Egr response
element (ERE) binding complex in brain extracts. We now report that
this complex contains a truncated isoform of Egr3 generated by use of
an alternate translation start site at methionine 106. Furthermore, the
ERE binding complex previously thought to contain full-length Egr3
includes several isoforms generated by initiation at other internal
methionines. Full-length and truncated (missing residues 1 to 105) Egr3
isoforms differ in the ability to stimulate transcription directed by a
tandem repeat of two EREs but not by a single ERE. Taken together, our
results indicate that alternative translation start sites are used to
generate Egr3 isoforms with distinct transcriptional properties.
 |
INTRODUCTION |
Recent studies indicate that the Egr
family of transcription regulatory factors plays an important role in
mediating changes in gene expression triggered by cell surface receptor
activation. Members of this family are induced as part of the
immediate-early gene response in a wide variety of cell types, allowing
them to regulate subsequent waves of gene expression (11).
The four identified members of this family share a highly conserved DNA binding domain that binds to a common DNA consensus sequence, referred
to as the Egr response element (ERE) (4, 35).
The high levels of expression of several Egr family members in adult
brain (40) combined with compelling evidence that the immediate-early gene response plays a critical role in synaptic plasticity (20, 24) have heightened interest in this
transcription factor family in the nervous system. Both
Egr1 and Egr3 mRNAs are robustly induced in
hippocampal dentate granule cells by afferent synaptic stimulation that
elicits long-term potentiation of this pathway, raising the possibility
that they mediate changes in gene expression critical for long-lasting
changes in synaptic efficacy (6, 39, 41). In addition, Egr
family members are also induced in brain neurons by natural stimuli
that induce plasticity (21, 22, 26, 27, 29, 38).
In recent studies aimed at defining the trans factors
expressed in brain that bind to the ERE, we found a previously
unidentified ERE binding complex (28). In gel shift assays
performed on hippocampal extracts, we detected three major ERE binding
complexes. The bands displaying the slowest and intermediate mobilities
were identified as complexes containing Egr1 and Egr3, respectively.
However, the third major complex eluded our initial attempts to
establish its identity. As the DNA sequence binding specificity of this novel complex matched that displayed by other Egr family members, we
suspected that it might represent a fifth Egr family member or a novel
isoform of one of the known members.
To determine whether this putative Egr family member was induced by
neuronal stimulation, we have in previous studies (28) examined its response to electrically induced seizure activity. In
contrast to the Egr1 complex, which reaches maximal levels at 1 h
and returns to basal levels by 4 h, this unidentified complex displayed a delayed response to stimulation similar to that found for
the Egr3 complex. Both of these delayed complexes were unchanged at
1 h, reached peak levels at 4 to 6 h, and returned to basal levels by 18 h. The parallel time course of these delayed ERE binding complexes prompted us to consider the possibility that the
novel complex represents a second isoform of Egr3. This view was
strengthened by the observation that incubation of recombinant Egr3
with the ERE probe yielded two complexes that comigrated with the
delayed bands detected in vivo. Since an N-terminal Egr3 antibody that
disrupted the upper band generated by recombinant Egr3 and its
endogenous counterpart did not affect the lower bands detected in vivo
or in vitro, we hypothesized that they contain a shorter isoform of
Egr3 lacking an N-terminal segment. Herein, we test this model and
provide evidence that several truncated Egr3 isoforms are generated in
vivo by utilization of multiple translation initiation sites.
Furthermore, we demonstrate that Egr3 isoforms that contain or lack the
N-terminal segment differ in the ability to activate transcription.
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MATERIALS AND METHODS |
Animal treatments.
Male Sprague-Dawley rats (200 to 250 g; Harlan, Indianapolis, Ind.) were used to assess the expression of
Egr3 under control conditions as well as following stimulation with
either maximal electroconvulsive seizure (MECS), administered as
described previously (28), or cocaine (30 mg per kg of body
weight, intraperitoneally). Wild-type and Egr3 knockout mice
were injected with pentylenetetrazol (50 mg kg
1,
intraperitoneally) to induce seizure activity. Egr3 knockout mice (37) and wild-type littermates were generously provided by Warren Tourtellotte and Jeff Milbrandt. Egr3 knockout
mice were generated by gene targeting that resulted in the deletion of
the DNA binding domain and a 3.4-kb portion of the 3' untranslated region of the Egr3 gene.
Antibody generation.
To generate antibodies directed against
an internal epitope of Egr3, a PCR-amplified Egr3 internal fragment
(Egr3-INT) spanning amino acids 101 to 189 was cloned into the pGEX-2T
(Pharmacia; Piscataway, N.J.) glutathione S-transferase
expression vector. Fusion protein purification, immunization, test
bleeds, and production bleeds were performed as described previously
(28).
Electrophoretic mobility shift assay.
Brain extracts were
prepared by Dounce homogenization as previously described
(28) except that we included pepstatin (1 mg
ml
1) in the harvest buffer. In the processing of rat
brains, tissue was homogenized immediately following dissection; mouse
brain tissue was processed in a similar fashion except that whole
brains were frozen after removal from the skull and then stored at
80°C until homogenization just prior to analysis by gel shift assay.
Two methods were used to prepare extracts from hEK-293 cells, with
similar results. In one method, Dounce homogenization was used to
obtain a high-salt extract of total cellular protein from hEK-293
cells. The other method (19) entails isolation of nuclei prior to the high-salt extraction step. Briefly, cells were rinsed and
then incubated in phosphate-buffered saline (PBS)-0.5 mM EDTA to
remove the cells from the dish. Cells were collected, pelleted, and
resuspended in PBS. The cells were then incubated for 15 min at 4°C
in 400 µl of a low-salt buffer (10 mM HEPES [pH 7.8], 10 mM KCl, 2 mM MgCl2, 0.1 mM EDTA, 1 µg of leupeptin
ml
1, 1 mM phenylmethylsulfonyl fluoride, 3 mM
dithiothreitol). Following incubation, 25 µl of 10% Nonidet P-40 was
added to the extract, which was then centrifuged at 14,000 × g for 10 min to pellet the nuclei. The cytoplasmic proteins
present in the supernatant were collected, aliquoted, and stored at
80°C. Next, the nuclei were incubated in a high-salt buffer (50 mM
HEPES [pH 7.4], 50 mM KCl, 300 mM NaCl, 0.1 mM EDTA, 10% [vol/vol]
glycerol, 1 mM phenylmethylsulfonyl fluoride, 3 mM dithiothreitol) for
30 min at 4°C to solubilize the DNA binding proteins. Extracts were
centrifuged at 14,000 × g for 10 min, and the
supernatant containing nuclear proteins was collected, aliquoted, and
stored at
80°C. Protein concentrations were determined by using a
bicinchoninic acid protein assay kit (Pierce, Rockford, Ill.).
Gel shift assays were conducted as described previously
(
28). Briefly, double-stranded oligonucleotides containing
the canonical
ERE, 5'-CTA GGA
GCG GGG GCG CTC ATG-3' (bold
letters indicate
the ERE), were end labeled and purified. In the
standard binding
reaction, the probe (0.1 to 1 ng of DNA corresponding
to ~40,000
cpm) is incubated at room temperature for 15 min with 10 to 20
µg of protein in the presence of calf thymus DNA (10 µg
ml
1). As indicated, this reaction was modified by
addition of 0.5
to 1 µl of antibody specific to Egr3-NT or Egr3-INT
(

Egr3-NT
or

Egr3-INT). The mutant ERE oligonucleotide, 5'-CTA GGA
GCG GGT GCG CTC ATG-3', which contains a single
nucleotide substitution
(underlined), was used to eliminate binding of
the nonspecific
band in mouse forebrain and hEK-293 cell
extracts.
Immunoblot analysis.
Samples were solubilized by addition of
0.5 volume of 3× sodium dodecyl sulfate (SDS) sample buffer (75 mM
Tris-HCl [pH 6.8], 2.5% SDS, 6% 2-mercaptoethanol, 12% glycerol)
followed by sonication if needed. Then 20 to 40 µg of extract protein
was separated by SDS-polyacrylamide gel electrophoresis, transferred,
and processed for immunoblotting as described previously
(28). Blots were probed with
Egr3-INT (1:500 dilution).
Plasmid constructs and mutagenesis.
For in vitro
transcription/translation experiments, Egr3 cDNA constructs were cloned
into pBluescript (Stratagene, La Jolla, Calif.). Recombinant Egr3
protein was synthesized using the Promega (Madison, Wis.) TnT kit. The
cytomegalovirus (CMV)-driven eukaryotic expression vector pCB6,
containing the full-length Egr3 insert (31), and the 1× ERE
and 2× ERE luciferase reporter constructs (7) were provided
by the laboratory of Jeff Milbrandt (Washington University, St. Louis,
Mo.).
To generate mutants that resulted in substitution of leucine or alanine
for Met, primers containing the desired mutations
were designed to
overlap a suitable, adjacent restriction site
if available. This
mutated primer and a vector-specific primer
were used in a PCR to
generate the desired mutation in Egr3. If
a convenient restriction site
was not present in the vicinity
of the mutation, we used splicing by
the overlapping extension
method (
12) to generate point
mutants. Mutated PCR products
were ligated into the vector of interest
after both were digested
with the appropriate restriction enzymes, and
the vector was additionally
treated with calf intestinal phosphatase
(New England Biolabs,
Beverly, Mass.). All ligation reactions were
carried out with
a Rapid DNA ligation kit (Boehringer Mannheim,
Indianapolis, Ind.).
All mutant Egr3 inserts were sequenced in their
entirety to verify
that the desired mutation had been achieved and that
no inadvertent
mutations were introduced during this
process.
Cell culture, transfection, and reporter assays.
We used
hEK-293 cells for the transfection and reporter experiments, as these
cells lacked detectable levels of Egr family expression in routine gel
shift or immunoblot assays. hEK-293 cells were maintained in
10-cm-diameter dishes at 37°C and 5% CO2 in Dulbecco
modified Eagle medium supplemented with 10% fetal bovine serum,
glutamine (2 mM), and a penicillin-streptomycin mixture (50 U
ml
1). At 24 h prior to transient transfection via
calcium phosphate precipitation (3), cells were passed into
either 10-cm (mutagenesis studies)- or 38-mm (reporter
studies)-diameter six-well dishes. For mutagenesis studies, cells were
transfected with 5 µg of Egr3 expression plasmid, rinsed 10 to
16 h later, and harvested 24 h after rinsing. For reporter
assays, we transfected cells with much lower levels of Egr3 expression
plasmid (50 ng) to ensure that the values obtained were in the linear
range of the luciferase assay. In addition, cells were transfected with
100 ng of reporter plasmid and 20 ng of
-galactosidase (
-Gal)
plasmid (to monitor transfection efficiency) and left undisturbed for
10 to 16 h after initiation of the transfection process. To
control for background reporter activity derived from endogenous
hEK-293 cell proteins, we conducted parallel transfection experiments
with the luciferase reporter, the
-Gal construct, and an empty CMV
vector. We consistently found that there is little detectable
background reporter activity in the hEK-293 cells under these
conditions. Cells were washed twice with warm medium and then fed with
fresh medium; 24 h later, cells were rinsed twice with warm PBS
and harvested in 1× reporter lysis buffer (Promega) and placed into
1.5-ml tubes on ice. Extracts were vortexed for 10 s and
centrifuged for 5 min at 14,000 × g. Supernatants were
collected, aliquoted, and used for both the luciferase and luminescent
-Gal assays, conducted according to the protocols of the
manufacturers (Promega and Clontech, Palo Alto, Calif.). For each, both
luciferase and
-Gal assays were performed in triplicate, and average
values were used in further analysis. To help control for variability
in transfection efficiency,
-Gal activity was used to normalize the
luciferase values obtained.
 |
RESULTS |
Egr3-INT recognizes both delayed ERE binding complexes.
To
test the possibility that the faster-migrating, delayed ERE DNA binding
complex detected in vivo contains a truncated isoform of Egr3, we
generated an antibody directed against an internal portion of the Egr3
protein that spanned amino acid residues 101 to 189 (
Egr3-INT [Fig.
1D]). To evaluate these antibodies, we first performed gel shift assays on recombinant Egr3 synthesized in
vitro. As described previously, incubation of recombinant Egr3 with the
ERE probe generates two bands, referred to as
and
(Fig. 1A),
and the
Egr3-NT antibody disrupts complex
but not complex
.
In contrast,
Egr3-INT inhibits both complexes. Thus, the
faster-migrating
complex likely contains a shorter form of Egr3
missing the N-terminal domain recognized by
Egr3-NT. Immunoblot
analysis of recombinant Egr3 and endogenous Egr3 in hippocampal
extracts provided direct confirmation of this interpretation (Fig. 1B).
Egr3-NT detects a single protein band in hippocampal extracts that
is induced following a seizure stimulus and comigrates with recombinant
Egr3. In contrast,
Egr3-INT detects two recombinant Egr3 protein
bands, an upper band or longer isoform also recognized by
Egr3-NT
and a lower band corresponding to a shorter form that reacts only with
Egr3-INT. As expected, both were induced following a seizure
stimulus (Fig. 1B), as found for the corresponding
and
gel
shift complexes (28).

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FIG. 1.
Identification of a truncated Egr3 isoform. (A)
Egr3-INT detects two Egr3 isoforms in a gel shift analysis of
recombinant Egr3 incubated either without antibody ( ) or with
Egr3-NT ( NT) or Egr3-INT ( INT). and refer to the
slower- and faster-migrating Egr3-containing complexes, respectively.
(B) Immunoblots of recombinant Egr3 run adjacent to control (Con) and
4-h post-MECS rat hippocampal extracts (HC) probed with Egr3-NT
(1:1,000 dilution) and labeled NT (left) and of similar extracts
probed with Egr3-INT (1:500 dilution) and labeled INT (right).
The band labeled Egr3 is recognized by Egr3-NT and Egr3-INT. In
contrast, the band labeled Egr3 NT is detected only by Egr3-INT,
indicating that it is truncated at the N terminus. (C) Egr3-INT
abolishes both delayed ERE binding complexes in vivo in ERE gel shift
assays using 32P-labeled ERE oligonucleotide probe on
control and MECS-treated hippocampal (left) or cortical (right)
extracts. and refer to Egr3-containing complexes. The
slowest-migrating band in the lane labeled NT (left) is a
supershifted Egr3 complex. The slowest-migrating band in all other
lanes is Egr1. The asterisk refers to a nonspecific band that does not
display sequence-specific ERE binding activity. (D) Schematic
representation of rat Egr3 (rEgr3) and the segments used to generate
the Egr3-NT (amino acids 1 to 100) and Egr3-INT (amino acids 101 to 189) antibodies. The zinc finger DNA binding domain is highlighted
in gray.
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To determine directly whether the

complex detected in vivo contains
the shorter Egr3 isoform, we added

Egr3-INT to the
gel shift
reaction mixture. As found for recombinant Egr3,

Egr3-INT
disrupted
binding of both

and

complexes whereas

Egr3-NT selectively
blocked the binding activity of complex

(Fig.
1C). Taken together,
these results provide compelling evidence that the

ERE binding
complex observed in vivo contains a truncated isoform of Egr3
that is
missing the N-terminal domain recognized by

Egr3-NT.
As expected,
the

Egr3-INT antibody does not affect the residual
nonspecific band
that migrates in proximity with the

complex.
In previous studies,
we found that this band does not contain
a specific ERE binding
complex, since it is displaced by a mutant
ERE oligonucleotide not
recognized by Egr family members (
28).
The truncated Egr3 isoform is widely expressed in the brain.
To assess whether the shorter Egr3 isoform is also expressed in other
brain regions or is restricted to the hippocampus, we conducted similar
studies of extracts harvested from the cerebral cortex. In gel shift
assays of cortical extracts from control and MECS-treated rats, we
observed that three distinct ERE binding complexes (Fig. 1C) were
increased following stimulation. This pattern of ERE DNA binding
activity closely mimics that observed in the hippocampus
(28). At 1 h following MECS, the uppermost complex is
induced, returning to control levels by 4 h, when elevations in
the
and
complexes are apparent. As found previously in studies
using hippocampal extracts, the slowest-migrating ERE binding complex
in the cortex contains Egr1, as its binding activity is selectively
abolished by an Egr1 antibody (data not shown), and the
complex
contains Egr3, since it is selectively eliminated by
Egr3-NT. In
addition, both
and
complexes are blocked by
Egr3-INT.
To determine if this pattern of ERE binding activities is also induced
by other stimuli, we performed gel shifts with the
ERE probe on
striatal extracts following administration of cocaine,
as this
treatment has been shown to trigger rapid increases in
both
Egr1 and
Egr3 mRNAs in this region (
1,
25,
41). In
these gel shift assays, we detected the same progression
of ERE
binding complexes and antibody sensitivities (data not shown)
found in the hippocampus and cortex following MECS stimulation.
Taken
together, the data from the hippocampus, cortex, and striatum
indicate
that neuronal stimulation elicits the delayed induction
of two distinct
Egr3-containing complexes; one corresponds to
an Egr3 isoform that
contains the N terminus, while the other
isoform does
not.
Egr3 knockout mice lack the
and
complexes.
The recent generation of Egr3 knockout mice (37)
enabled us to perform a rigorous test of our interpretation of these
antibody studies. If our view is correct, then the
and
complexes should be absent in extracts prepared from these mice. The
pattern of ERE binding complexes detected in forebrain extracts
prepared from wild-type mice was identical to that observed in the rat brain (Fig. 2A). However, as predicted,
extracts prepared from Egr3 knockout mice lacked the
and
complexes, which were also abolished by the
Egr3-INT antibody in
extracts prepared from wild-type mouse brain (Fig. 2A). Of note, the
Egr1 complex was unchanged in both wild-type and Egr3
knockout mice. Thus, these studies support the conclusion that the
and
complexes found in both rat and mouse brain correspond to Egr3
isoforms that include and lack the N terminus, respectively.

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FIG. 2.
Egr3 knockout mice lack and complexes. (A) Pattern of ERE binding complexes detected in 4-h
postseizure forebrain (FB) extracts from wild-type (+/+) and
Egr3 knockout ( / ) mice. In the right lane, labeled
INT, wild-type extracts were incubated with Egr3-INT. and refer to specific Egr3-containing complexes in panels A and B. We
eliminated binding of the nonspecific band in mouse brain extracts by
inclusion of 100-fold excess of unlabeled mutant ERE oligonucleotide.
(B) Mutation of Met 106 abolishes expression of truncated Egr3 isoform,
determined by a gel shift assay of recombinant Egr3 synthesized in
vitro from wild-type (wt) and mutated (M106L) Egr3 cDNA
templates. (C) Immunoblot of recombinant extracts containing wild-type
or mutated (M106L) Egr3 probed with Egr3-INT (1:500 dilution). The
asterisks refer to cross-reacting proteins that are present in the
rabbit reticulocyte preparations. (D) Schematic representation of rat
Egr3 protein depicting Met residues 1, 13, 49, and 55 within the NT
epitope and Met residues 106, 129, and 140 within the INT epitope. The
zinc finger DNA binding domain is shown in gray.
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|
Mutation of Met 106 blocks formation of the truncated Egr3 isoform
in vitro.
Since both Egr3 isoforms are expressed in vitro from the
same cDNA template, we suspected that the shorter isoform is generated via a posttranscriptional mechanism rather than alternative splicing. Either proteolytic cleavage of full-length Egr3 or utilization of an
alternative translation start site could yield a truncated Egr3 isoform
with an N terminus located just prior to or within the internal segment
targeted by
Egr3-INT (amino acids 101 to 189). However, we favored
the latter alternative since we reliably obtain the shorter isoform in
vitro despite the presence of protease inhibitors. Furthermore,
prolonging the incubation does not lead to production of higher levels
of the shorter isoform at the expense of the longer isoform, as might
be expected if generation of the shorter isoform depended on
proteolytic cleavage of the longer one.
To test the possibility that the shorter isoform is generated by
utilization of an alternative translation start site, we
checked
whether mutating candidate Met residues eliminated production
of this
isoform in vitro. We focused on the Met residues located
at positions
106, 129, and 140 since they are conserved in rats
and mice and could
serve as alternative translation initiation
sites that generate Egr3
isoforms recognized by

Egr3-INT but
not

Egr3-NT. We first tested
Met 106 by generating an Egr3 point
mutant construct, Egr3M106L,
containing a substitution of Leu
for Met at residue 106. Recombinant
Egr3 was synthesized in vitro
from both wild-type and Egr3M106L mutant
constructs and used in
immunoblot and gel shift experiments.
Immunoblots probed with

Egr3-INT demonstrated that the M106L
mutation led to a selective
loss of the shorter isoform (Fig.
2C).
Also, gel shift assays
revealed that this mutation abolished the
Egr3-containing complex

(Fig.
2B). These results indicate that the
shorter Egr3 isoform
is made by initiating translation at M106.
Unexpectedly, we found
that the

Egr3-INT antibody detected two
lower-molecular-weight
protein bands in immunoblots of Egr3M106L
recombinant extracts.
Furthermore, two additional ERE binding complexes
were observed
in the gel shift assay. Presumably, elimination of the
preferred
start site at M106 favors utilization of the downstream Met
residues
at positions 129 and 140. Examination of additional mutants
described
below supports this
inference.
Use of additional translation start sites.
In the course of
conducting these studies, we optimized conditions for separating the
Egr3 DNA binding complexes and noticed that a complex previously
thought to contain only full-length Egr3 could be reliably resolved
into three distinct complexes,
1,
2, and
3 (Fig. 3). In
addition to the initial Met, there are three Met residues at positions
13, 49, and 55 located within the N-terminal segment targeted by
Egr3-NT (Fig. 2D). Since our analysis of the
complex indicates
that it contains a shorter Egr3 isoform derived from initiation at Met
106, we wondered whether the
complex might include additional
complexes formed by truncated versions of Egr3 that start at Met
residues near the N terminus. To address this possibility, we made a
series of mutations targeting the potential internal translation start
sites and examined their effects on the pattern of ERE binding
complexes generated in vitro.
In initial studies, we demonstrated that deletion of Met 1 eliminates
the

1 complex (Fig.
3), which
represents the ERE binding
complex containing a full-length Egr3. Using
this construct, Egr3

M1,
as a template, we generated a series of
constructs with point
mutations at the next five Met residues (at
positions 13, 49,
55, 106, and 129). The M13L mutation abolished
formation of the

2 complex. Since we had already shown that
formation of the
complex was dependent on M106, we predicted that
either M49 or
M55 would be critical for generating the

3 complex.
Unexpectedly,
analysis of the M49L and M55L mutants (Fig.
3) revealed
that each
individual mutation did not completely abolish the

3
complex.
However, the M49L mutation partially blocked the

3 band
whereas
the M55L mutant had little or no effect. In contrast, the
M49A/M55A
double mutant resulted in a complete abolition of the

3
complex
(Fig.
3). These findings suggest that both M49 and M55 are
utilized
and that we are unable to resolve their corresponding
complexes.
Accordingly, we refer to the

3 complex as being derived
from
M49/55.

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FIG. 3.
Mutation of specific Met codons abolishes expression of
Egr3 isoforms in vitro. (A) Pattern of ERE binding complexes detected
in wild-type mouse forebrain (FB), included to highlight the close
similarity between Egr3 complexes expressed in vivo and in vitro. (B
and C) Gel shift assays of recombinant Egr3 synthesized in vitro from
the mutated versions of the Egr3 cDNA indicated above the
lanes. All Egr3 cDNAs shown in panels B and C are in the
Egr3 M1 vector backbone and thus do not express Egr3 1.
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As shown in Fig.
2B, the Egr3M106L mutation eliminates the

complex
as well as enhancing synthesis of faster-migrating ERE
binding
complexes thought to reflect initiation at M129 and M140.
Close
inspection of the complexes detected in vivo as well as
in vitro
revealed the consistent presence of a minor band that
migrates ahead of
the

complex and comigrates with the major
complex generated by the
M106L mutant. This band, labeled

, is
induced by neuronal
stimulation (Fig.
1C) disrupted by

Egr3-INT
(Fig.
1C and
2A) and
absent in
Egr3 knockout mice (Fig.
2A), indicating
that it
is a bona fide, albeit minor, ERE binding complex present
in vivo. It
is abolished by the M129L mutation, indicating that
it contains a
truncated form of Egr3 initiated at this Met. Furthermore,
these
findings support our contention that the M106L mutation
enhances
initiation at distal Met residues. Although this mutational
analysis
provides strong evidence that the multiple Egr3 complexes
detected in
vivo reflect translation initiation at internal Met
residues, we wanted
to examine whether these in vitro findings
accurately describe the
situation in intact
cells.
Egr3 isoform expression abolished by start site mutations in intact
cells.
In preliminary gel shift experiments, we found that
transient transfection of hEK-293 cells with the full-length Egr3
construct (CMVEgr3wt) yielded a pattern of Egr3 complexes (Fig. 4A)
similar to that found in the brain. To assess the effect of mutating
putative start sites in intact cells, we prepared a series of point
mutants (M13L, M49L, M49A/M55A, and M106L) in the Egr3
M1 backbone
used for the in vitro experiments. Cells transfected with the
CMVEgr3
M1 construct lacked the full-length Egr3
1 complex (Fig.
4A). The M13L and M106L mutations
abolished the
2 and
complexes, respectively (Fig. 4B). Also, the
M49L mutation partially suppressed the
3 complex, while the
M49A/M55A double mutant completely abolished this band (Fig. 4B).

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FIG. 4.
Mutagenesis studies of Egr3 in intact cells. (A) ERE
binding complexes detected in hEK-293 cell extracts that were
untransfected (UT) or transfected with CMVEgr3wt (wt [wild-type]) or
M1 cDNA. (B) Autoradiograph of a similar gel shift experiment
performed on hEK-293 cell extracts transfected with CMVEgr3M13L, M49L,
M49A/M55A, and M106L cDNAs. The mutated constructs in panel B are in
the CMVEgr3 M1 backbone and thus do not express Egr3 1. The complex appears when M106 is mutated to Leu. (C) Immunoblot analysis
using Egr3-INT (1:500 dilution) performed on the nuclear extracts
used for gel shift assays. Egr3-INT detects two immunoreactive bands
in CMVEgr3wt-transfected cells that correspond to the (upper) and
(lower) gel shift complexes. The M106L mutation abolishes
expression of the lower band and leads to the generation of a
faster-migrating band that corresponds to that complex. (D) Schematic
representation of the translation start sites of the Egr3 isoforms
detected in vivo, Egr3 1 (M1), 2 (M13), 3 (M49/55), (M106),
and (M129). The zinc finger DNA binding domain is indicated in
gray.
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In previous immunoblot studies of recombinant Egr3 with

Egr3-INT, we
found that the M106L mutation led to a selective loss
of the truncated
Egr3 isoform that corresponds to the

complex
in gel shifts. To test
whether the CMVEgr3M106L mutant had a similar
effect in intact cells,
we performed immunoblotting with

Egr3-INT
on the transfected hEK-293
extracts used for the gel shift studies.
In contrast to CMVEgr3wt,
which drives expression of two

Egr3-INT
immunoreactive bands,
CMVEgr3M106L-transfected cells exhibited
a selective loss of the
shorter Egr3 isoform (Fig.
4C). Also,
in M106L mutant extracts,

Egr3-INT detects a faster-migrating
band that corresponds to the

complex. Of note, immunoblots performed
on extracts of the
CMVEgr3

M1, CMVEgr3M13L, and CMVEgr3M49A/M55A
mutants revealed that
neither of these mutations completely abolished
immunoreactivity of the
upper band recognized by

Egr3-INT. Although
we detect slight
alterations in the mobility of the upper band
in immunoblots of these
mutant extracts, the multiple Egr3 isoforms
present could not be
consistently resolved into discrete bands
(Fig.
4C). In summary,
studies using intact cells corroborate
our in vitro observations that
the Egr3 isoforms (Fig.
4D) identified
in vivo are generated through
initiation at multiple translation
start sites, i.e., M1, M13,
M49/M55, M106, and
M129.
Egr3 isoform transcriptional activity.
Since the domains of
Egr3 mediating transcriptional activation have not been defined, we
wanted to test whether the truncated Egr3
isoform is
transcriptionally active and, if so, how it compares to full-length
Egr3 (Egr3
1). As an initial attempt to express full-length Egr3 in
the absence of truncated isoforms, we altered the sequence surrounding
the initial start codon such that it contains the two most important
Kozak consensus residues (A at
3 and G at +4 [17]).
Although this increased the proportion of the
1 complex, substantial
amounts of the
3 and
complexes were generated as well.
Accordingly, we prepared the CMVEgr3M49A/M106A mutant construct in the
CMVEgr3wt backbone that retains Met residues at positions 1, 13, 55, and 129. To express Egr3
(Fig. 5C), we generated CMVEgr3
1-105/M129L, which contains the preferred Kozak residues surrounding the Met 106 start codon and a mutated M129. To
test whether these constructs could successfully drive expression of
the desired Egr3 isoforms, we transfected hEK-293 cells with equal
amounts of the cDNAs encoding Egr3
1 and Egr3
and prepared immunoblots of nuclear extracts from these cells. As shown in Fig. 5C,
Egr3
1 and Egr3
are expressed at comparable levels when equivalent
amounts of their respective cDNAs are transfected into cells. Since an
immunoblot does not allow us to determine the relative expression of
each Egr3
isoform, we performed parallel gel shift experiments on
these extracts to monitor the individual expression of Egr3 isoform DNA
binding activity. The CMVEgr3M49A/M106A construct achieved the desired
result, yielding predominant expression of the
1 complex and only
residual expression of Egr3
2 (Fig. 5D). Thus, we refer to this form
as Egr3
1/
2.

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|
FIG. 5.
Transcriptional activity of Egr3 isoforms. (A) Schematic
representation of the expression and reporter vectors used in the
reporter assays. The 1X ERE and 2X ERE reporter constructs contained
either one or two copies of an ERE (GCG GGG GCG) upstream of the
firefly luciferase gene. (B) Bar graph showing fold induction in
luciferase activity induced by transfection with either
CMVEgr3M49A/M106A (encoding Egr3 1/ 2) or CMVEgr3 1-105/M129L
(encoding Egr3 ) over background reporter activity (taken from
extracts of hEK-293 cell transfected with an empty CMV vector) for the
2X (left) and 1X (right) EREs. Error bars represent standard errors of
the means. Statistical analysis of these data demonstrate that the Egr3
constructs tested differ significantly in their effects on the 2X ERE
but not the 1X ERE (P < 0.0005 and P > 0.5, respectively; Student's t test). (C) Immunoblot
of untransfected hEK-293 cells run adjacent to hEK-293 cells
transfected with 5 µg of CMVEgr3M49A/M106A (encoding Egr3 1/ 2)
or CMVEgr3 1-105/M129L (encoding Egr3 ) probed with Egr3-INT
(1:500 dilution). (D) Representative gel shift experiment using a
32P-labeled ERE oligonucleotide probe on extracts of
hEK-293 cells untransfected (UT) or transfected with 5 µg of
CMVEgr3wt (wt [wild type]) or CMVEgr3M49A/M106A ( 1/ 2).
|
|
We next examined the ability of Egr3

1/

2 and Egr3

to drive
expression of luciferase reporter constructs (Fig.
5A) containing
either one (1X ERE) or two (2X ERE) EREs in the proximal promoter
region. When we compared these isoforms on the 2X ERE promoter,
we
found that Egr3

1/

2 was more effective than Egr3

at driving
reporter activity (Fig.
5B). In contrast, when we tested Egr3
isoform
transcriptional output on a promoter containing a single
copy of the
ERE, Egr3

1/

2 expression and Egr3

expression had
comparable
effects (Fig.
5B). Thus, these data suggest that the
transcriptional
activity of the Egr3

1/

2 and Egr3

isoforms display
different
properties depending on the promoter
context.
 |
DISCUSSION |
In this study, we conducted experiments aimed at identifying a
major ERE binding complex expressed in the brain, defining how it is
generated, and understanding its role in regulating ERE-mediated
transcription. In the first phase of the study, we confirmed our
hypothesis that the unidentified ERE complex contained a truncated form
of Egr3 missing the N terminus. This conclusion is based on its absence
from extracts prepared from Egr3 knockout mice as well as studies with
an antibody directed to an internal segment of Egr3. In the second
phase of the study, we obtained evidence that the shorter isoform is
generated by utilization of an internal translation start site located
at M106 and that additional isoforms of Egr3 are generated by
utilization of other Met residues as well. In the last phase of this
investigation, we compared the functional activities of Egr3 isoforms
that contain or lack the N-terminal segment and found that they display
distinct transactivation properties.
Although we initially identified multiple Egr3 isoforms in hippocampal
extracts, gel shift studies on extracts prepared from other brain
regions indicate that they express a similar array of truncated
isoforms. In addition, heterologous expression of Egr3 in hEK-293 cells
generated a pattern of Egr3 binding complexes that was
indistinguishable from the pattern displayed in the brain. In the
periphery, Egr3 is induced by T-cell activation (23). In
preliminary studies, we have detected a similar pattern of Egr3
expression in a murine T-cell hybridoma, 2B4.11. Accordingly, coexpression of full-length and truncated Egr3 isoforms appears to be a
general feature of this transcript.
Previous in situ hybridization studies have demonstrated induction of
all four Egr family members in the hippocampus following electroconvulsant stimulation (2, 5, 8, 41). Thus, it is
surprising that all of the major ERE binding complexes observed in gel
shift studies contain only Egr1 and Egr3. The absence of prominent Egr2
and Egr4 binding complexes in these assays could in principle reflect
low levels of protein expression or inhibitory factors that block
binding activity. In any case, these findings suggest that Egr1 and
Egr3 are the dominant family members mediating ERE-driven transcription
in the hippocampus.
The demonstration that mutations targeting individual Met residues
block expression of Egr3 isoforms provides compelling evidence that
they are generated by utilization of internal translation start sites.
Although viruses commonly utilize this mechanism to express variant
proteins, it has been seldom implicated with regard to cellular
proteins (32). A priori initiation at internal start sites
can be attributed either to internal entry of the ribosomal complex,
instead of its attachment to the 5' cap, or to leaky ribosomal
scanning, i.e., ignoring potential start sites presumably because the
flanking sequence deviates from the rules governing faithful
initiation. As shown in Table 1, the
leaky scanning mechanism may apply to Egr3. However, it is unclear if this fully accounts for the ability of the translation initiation complex to skip the first Met. Substituting nucleotides at key sites
surrounding the initial start codon to comply with these rules enhanced
usage of the Egr3 initial Met but did not prevent generation of
truncated products.
Although alternative splicing is widely recognized as a mechanism used
to generate multiple protein isoforms from a single transcription
factor gene, only a few instances in which alternative translation
start sites are utilized have been reported. Interestingly, two members
of the C/EBP family, C/EBP
(9) and C/EBP
(30), employ this strategy to generate truncated versions
with markedly different transcriptional properties. As the splicing
mechanism is not available to these intronless genes, the alternative
translation start site strategy appears to be used instead. This
teleological rationale presumably applies to Egr3 as well, since it
contains only two exons, as found for all Egr family genes
(8).
Our comparison of the functional activities of Egr3 isoforms that
retain or lack the N-terminal segment indicates that deletion of this
segment has little effect on Egr3's ability to stimulate transcription
of genes containing a single copy of the ERE in their promoter. In
contrast, deletion of the N-terminal segment impairs its ability to
stimulate transcription when two copies of the ERE are present.
Accordingly, the N-terminal domain appears to play an important role in
boosting expression of genes containing multiple EREs. Based on these
findings, it is tempting to speculate that altering the ratio of
Egr3
and Egr3
isoforms may provide a mechanism for modulating Egr
target genes with multiple EREs such as platelet-derived growth factor
A chain (15, 33), prohormone convertase 2 (13),
and synapsin I (36) without affecting those containing a
single ERE, e.g., platelet-derived growth factor B chain
(14), transforming growth factor (10, 16),
luteinizing hormone beta chain (18), and FasL
(23). In this scenario, shifts in the functional activities
of full-length and truncated Egr3 isoforms could be achieved directly
by changes in their protein levels. Indeed, preliminary findings
(26a) suggest that there is some developmental regulation of
the pattern of Egr3
isoform expression. Egr3
1 is present at
relatively high levels in embryonic day 17 rat cortex, and its levels
decrease to near adult levels by postnatal day 8. In contrast, Egr3
2
DNA binding activity is low in embryonic day 17 cortex but its levels
are significantly increased in postnatal day 8 cortex. Alternatively,
as the N-terminal truncation does not impinge on the domain mediating
suppression of Egr3 by NAB proteins (31, 34) located just N
terminal to the DNA binding domain, it is conceivable that changes in
the relative sensitivities of full-length and truncated Egr isoforms to
NAB proteins could be used to alter their activities.
Although the Egr family DNA binding domain has been extensively
characterized, little is known about how Egr family members act to
stimulate the transcriptional apparatus. Our initial analysis of
naturally occurring truncations of Egr3 has revealed interesting differences in the activation properties of these isoforms and underscores the need to conduct more extensive studies aimed at defining the activation domains contained within these proteins and how
they interact with the transcriptional apparatus. Progress in this
direction will be helpful in elucidating the functional significance of
the Egr3 isoforms expressed in vivo as well as in understanding how the
Egr family orchestrates changes in gene expression in response to
cellular stimulation.
 |
ACKNOWLEDGMENTS |
This study was supported by Public Health Service grants from the
National Institute of Drug Abuse (DA00266 and DA00358 [J.M.B.] and
DA05753 [K.J.O.]) and an NARSAD independent investigator award (J.M.B.).
We thank E. Eipper, D. Ginty, S. S. Wang, and P. Worley for use of
equipment, helpful discussions, and advice; D. Ahn, Y. S. Kwon,
and W. Z. Tang for expert technical assistance; Jeff Milbrandt and
Warren Tourtellotte for generously providing reagents and samples; and
D. Ginty for critical reading of the manuscript.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Department of
Neuroscience, WBSB 908, Johns Hopkins University School of Medicine, 725 N. Wolfe St., Baltimore, MD 21205. Phone: (410) 955-2500. Fax:
(410) 614-6249. E-mail: jbaraban{at}jhmi.edu.
 |
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