Plant Physiol. (1999) 120: 491-500
Identification of a cis-Regulatory Element Involved
in Phytochrome Down-Regulated Expression of the
Pea Small GTPase
Gene pra21
Takehito Inaba,
Yukio Nagano,
Toshihiro Sakakibara, and
Yukiko Sasaki*
Laboratory of Plant Molecular Biology, Graduate School of
Bioagricultural Sciences, Nagoya University, Nagoya 464-8601,
Japan
 |
ABSTRACT |
The pra2 gene encodes
a pea (Pisum sativum) small GTPase belonging to the
YPT/rab family, and its expression is down-regulated by light, mediated
by phytochrome. We have isolated and characterized a genomic clone of
this gene and constructed a fusion DNA of its 5
-upstream region in
front of the gene for firefly luciferase. Using this construct in a
transient assay, we determined a pra2 cis-regulatory
region sufficient to direct the light down-regulation of the luciferase
reporter gene. Both 5
- and internal deletion analyses revealed that
the 93-bp sequence between
734 and
642 from the transcriptional
start site was important for phytochrome down-regulation.
Gain-of-function analysis showed that this 93-bp region could confer
light down-regulation when fused to the cauliflower mosaic virus 35S
promoter. Furthermore, linker-scanning analysis showed that a 12-bp
sequence within the 93-bp region mediated phytochrome down-regulation.
Gel-retardation analysis showed the presence of a nuclear factor that
was specifically bound to the 12-bp sequence in vitro. These results
indicate that this element is a cis-regulatory element
involved in phytochrome down-regulated expression.
 |
INTRODUCTION |
Plants use light not only as an energy source for photosynthesis
but also as an environmental signal. When a plant germinates in soil
and is exposed to light after elongating its stem, the stem elongation
is immediately repressed, and the leaves expand, turn green, and
photosynthesis is initiated. Many of these changes are caused by the
regulation of gene expression mediated by photoreceptors such as
phytochrome. A pea (Pisum sativum) small GTPase gene, pra2, which belongs to the YPT/rab family (Nagano et al.,
1993
), is one of the genes whose expression is mediated by phytochrome (Yoshida et al., 1993
). The pra2 gene is mainly expressed in
the growing zone of etiolated epicotyls, and its expression is
repressed when the plant is illuminated (Nagano et al., 1995
). An
interesting character is that the expression of this gene is
down-regulated by phytochrome and probably involved in the
morphogenesis of etiolated seedlings after germination. Small GTPases
are molecular switches that are turned on by GTP and off by the
hydrolysis of GTP to GDP. Members of the YPT/rab family play important
roles during intracellular transport. Thus, the pra2 protein
may participate in vesicle transport occurring in stem elongation of
etiolated seedlings (Nagano et al., 1995
).
There are many genes up-regulated by phytochrome, such as
rbcS (Sasaki et al., 1983
) and Lhcb (Kehoe et
al., 1994
), and several cis-regulatory regions involved in
light-enhanced expression have been characterized (Terzaghi and
Cashmore, 1995
). However, there are not so many genes down-regulated by
phytochrome, compared with those up-regulated. A few of these genes
have been analyzed for cis-regulatory elements. Although
detailed analysis of a PHYA promoter has revealed a
phytochrome-repressible element, RE1 (Bruce et al., 1991
), the gene for
the putative repressor RF1, has not yet been cloned. Recently,
Weatherwax et al. (1998)
showed that the phytochrome response of the
NPR1 gene was primarily mediated by the alteration of ABA
levels and identified two elements necessary for phytochrome- and
ABA-mediated responses. Although other genes such as tubB1
(Tonoike et al., 1994
), AS1 (Nagi et al., 1997
), and
Athb2 (Carabelli et al., 1996
) have also been reported as light down-regulated genes, we do not have as much information about
down-regulation as about up-regulation.
We have been interested in the expression of the pra2 gene.
Here we have examined the cis-regulatory element
contributing to light down-regulation of the pra2 gene by
transient assay using a reporter gene and etiolated pea
stems.
The accession number for the sequence reported in this article is
AB007911.
 |
MATERIALS AND METHODS |
Characterization of the pra2 Gene
The genomic clone of the pra2 gene was isolated from a
pea (Pisum sativum) genomic library (Stratagene) using the
pea pra2 cDNA (Nagano et al., 1993
) as a probe. The plaque
hybridization and DNA sequencing were conducted as described previously
(Nagano et al., 1993
). The nucleotide sequence reported will appear in the EMBL, GenBank, and DDBJ nucleotide sequence databases under the
accession no. AB007911. Primer-extension analysis was performed by the
method reported previously (Nagano et al., 1991
). The synthetic oligonucleotide for primer-extension analysis was
5
-ACGGTTGTTGAATTACCGGTGTTAATAGAG-3
.
Plant Material, Particle Bombardment, and Light Treatment
Pea (cv Alaska; Snow Brand Seed, Sapporo, Japan) seeds were soaked
in water and sowed in a plastic pot separately. The pot (14 mm in
diameter) had a polyethylene net at its lower end and was filled with
rock wool and placed in an irrigated vat. Seedlings were grown in the
dark for 5 or 6 d at 25°C. A seedling was set horizontally in
the bombardment device (model GIE-III, Tanaka Co. Ltd., Sapporo,
Japan), which was described in detail by Takeuchi et al. (1992)
. To the
growing zone of the etiolated stem (between 0 and 1 cm from the top of
the hook), 1.5- to 3.0-µm gold particles were bombarded once. The
gold particles were coated with a mixture of two kinds of plasmids, a
plasmid containing one of the pra2:LUC constructs and a
plasmid containing a 35S-GUS construct. Five micrograms of each plasmid
was mixed with 2-mg gold particles and suspended in 200 µL of
ethanol. A 4-µL aliquot of the suspension was used for each
bombardment. We performed all of the steps during bombardment in a
darkroom with a dim-green safety light. After bombardment, the plant
was returned to the irrigated vat and incubated in continuous white
light or darkness for 12 h at 25°C. White light was provided by
white fluorescent tubes at an intensity of 70 µmol
m
2 s
1 (measured by a
quantum sensor, model LI-190SA, LI-COR, Lincoln, NE).
Equipment for red and far-red irradiation was the same as that
described previously (Yoshida et al., 1993
). For brief red-light irradiation, monochromatic light with a peak emission at 660 nm was
supplied at an intensity of 30.5 µmol m
2
s
1 (measured by a quantum sensor, model
LI-190SA, LI-COR) for 2 min. For brief far-red light irradiation,
monochromatic light with a peak emission at 750 nm was supplied at an
intensity of 36.5 µmol m
2
s
1 (measured by thermopiles, model MIR-100Q,
Mitsubishi Oil Chemicals, Tokyo, Japan) for 5 min. A pair of modified
slide projectors (Cabin III) each equipped with a 300-W halogen lamp
(Philips, Eindhoven, The Netherlands) was used as a source. This light
was filtered through a combination of a red-interference filter
(maximum wavelength = 660 nm; DIF-BPF-2, Vacuum Optics, Tokyo, Japan)
and a heat-cut filter (CF-B) to obtain red light and through a far-red
interference filter (maximum wavelength = 750 nm; DIF-BPF-2) and a
long-wavelength heat-cut filter (CF-A) to obtain far-red light.
Measurements of Enzyme Activities
A stem of the bombarded pea seedling (between 0 and 1 cm from the
top of the hook) was ground in liquid N2 using a
chilled mortar and pestle. The powder was dispensed into a
microcentrifuge tube and mixed with 300 µL of the buffer consisting
of 100 mM potassium phosphate, pH 7.8, 1 mM
DTT, 1% Triton X-100, and 1 mM EDTA and then
centrifuged at 15,000g at 4°C for 5 min. The supernatant was frozen at
80°C until the enzyme assay was
conducted. LUC assays were performed as described by Miller et al.
(1992)
using the Pica Gene LUC assay kit (Wako, Osaka, Japan). Photon emission derived from LUC activity was counted by AUTO LUMAT LB953 (Berthold, Bad Wildbad, Germany). GUS activity was measured
by the method of Jefferson et al. (1987)
, using
4-methylumbelliferyl
-D-glucuronide
(Wako) as the substrate. Resulting 4-methylumbelliferone concentrations
were determined by Fluoroskan II (Labsystems, Research Triangle
Park, NC). To the reaction mixture, 10% methanol was added to
enhance GUS activity (Kosugi et al., 1990
).
4-Methylumbelliferone solutions dissolved in 0.2 M Na2CO3
were used as the standards. Proteins were measured using the
DC Protein Assay kit (Bio-Rad). Background activities from
plants bombarded with gold particles only were subtracted from each LUC
and GUS value. All LUC values were normalized to the corresponding GUS
values. Samples of at least four bombardments were independently
assayed for each construct. The mean values were normalized to that of
the full-length construct (PL1) kept in the dark.
Construction of pra2-LUC Plasmids
The plasmids were constructed by four methods as described below.
(1) The pra2 upstream regions were amplified by cloned Pfu
(Pyrococcus furiosus) DNA
polymerase (Stratagene) using two primers containing HindIII
and NcoI sites of their 5
ends, respectively. The
NcoI site corresponds to the initiation codon of the
pra2 gene. The HindIII site corresponds to the
upstream region. For the creation of LS constructs, each upstream
primer had 6-bp mutations corresponding to the PstI site on
different positions. The amplified fragments were subcloned into the
EcoRV site of the pZErO-2.1 vector (Invitrogen, San Diego,
CA), and digested with HindIII and NcoI. DNA
fragments were electrophoresed, purified by a DNA-extraction kit
(Pharmacia Biotech), and subcloned into the
HindIII-NcoI sites of the pBI221-LUC+ vector (a
gift from Dr. K. Hiratsuka, NAIST Graduate School of Biological
Science, Nara, Japan). HindIII-NcoI digestion of
pBI221-LUC+ plasmid yielded a 35S promoter-less vector. All subcloned
regions of each construct were confirmed by DNA sequencing. The
constructs PL1, PL3, PL4, PL4A, and PL5, and all LS constructs, were
created by this method.
(2) The constructs PL2, PL6, PL7, PL8, and PL4C were amplified by
LA-Taq (Takara, Otsu, Japan)-mediated inverse PCR using PL1
as a template. The amplified fragments were blunt ended by cloned Pfu
DNA polymerase and self-ligated.
(3) To create the pra2-35S90-LUC (GF) plasmid, the
pra2 upstream regions were amplified by cloned Pfu DNA
polymerase using two primers containing the EcoRV and
PstI site, respectively. The amplified fragments were
subcloned into pZErO-2.1 vector as described above and digested with
EcoRV and PstI. The purified DNA fragments were
subcloned into the EcoRV-PstI sites of
pBI221-LUC+. EcoRV-PstI digestion of the
pBI221-LUC+ plasmid yielded a 35S90-LUC vector.
(4) To create the PL4B construct, the pra2 upstream regions
were amplified by cloned Pfu DNA polymerase using two primers containing the HindIII and PstI sites of their 5
ends. The amplified fragments were subcloned into the pZErO-2.1 vector
as described above and digested with HindIII and
PstI. The purified DNA fragments were subcloned into the
HindIII-PstI digest of LS5 carrying the LUC gene.
In all of the plasmids used in this study, we measured the luminescence
of the Escherichia coli culture containing each construct and selected a representative clone for plasmid purification to exclude
mutations occurring on the LUC gene. All plasmids were purified using a
plasmid extraction kit (Qiagen, Chatsworth, CA).
Extraction of Protein and Immunoblotting
Total protein for immunoblotting was extracted by grinding tissue
with a mortar and pestle at room temperature with sand together with
0.3 mL of buffer and three stem pieces (between 0 and 1 cm from the top
of the hook). The buffer contained 125 mM Tris-HCl, pH 6.8, 6% SDS, and 20% glycerol. The mixture was heated at 100°C for 3 min
and centrifuged. The supernatant protein was separated by SDS-PAGE,
blotted onto a nitrocellulose membrane, probed with monoclonal IgG
against the pra2 protein (Nagano et al., 1995
) and goat
anti-mouse IgG conjugated to peroxidase (Bio-Rad), and developed with
an ECL kit (Amersham).
Preparation of Nuclear Extract
Nuclear extracts were prepared by a modification of the method
described by Ishiguro and Nakamura (1992)
. Pea seedlings were grown in
darkness for 6 d. For light-treated samples, seedlings were
exposed to white light for 6 h before nuclear extraction. The
upper region of pea epicotyls (1-cm section from the top of the hook,
20 g) was cut into pieces. Then they were homogenized with 250 mL
of homogenization buffer containing 10 mM Pipes-KOH, pH 7.0, 1 M hexylene glycol, 10 mM
MgCl2, 5 mM
-mercaptoethanol, 1 mM PMSF, 8 µM pepstatin A, and 2.4 µM leupeptin, in a homogenizer (Hitachi, Tokyo, Japan).
The homogenates were filtered through Miracloth (Calbiochem). Nuclei
were pelleted from the homogenate by centrifugation at
2,700g for 15 min, resuspended in 50 mL of washing buffer
consisting of 50 mM Tris-HCl, pH 7.5, 10 mM MgCl2, 20% glycerol,
and 5 mM
-mercaptoethanol, and then
centrifuged at 5,200g for 15 min. Washing and centrifugation
were repeated three times. Nuclei were resuspended in 3 mL of nuclear
lysis buffer consisting of 15 mM Hepes-KOH, pH
7.5, 1.25 M KCl, 5 mM MgCl2, 2.5 mM EDTA, 1 mM DTT, 1 mM PMSF, 8 µM pepstatin A, and 2.4 µM leupeptin, with gentle stirring. Particulate
material was pelleted by centrifugation at 5,200g for 15 min
and then at 100,000g for 1 h. The supernatant was
desalted by dialysis. The sample was then centrifuged at
12,000g for 15 min, and the supernatant was collected and
stored at
80°C until the assay was performed. Proteins were
measured using the DC Protein Assay kit (Bio-Rad).
Gel-Retardation Assay
The gel-retardation assay was performed by the method described by
Shimizu et al. (1996)
with some modification. Synthetic oligonucleotides for gel-retardation assay were as follows:
5
-GTCTGAGGATTTTACAGTAATAAAGAAACGA-3
(WT1) and
5
-TCGTTTCTTTATTACTGTAAAATCCTCAGAC-3
(WT2). The 5
end of a 31-bp
WT1 DNA probe was labeled by incubation with
[
-32P]ATP and T4 polynucleotide kinase and
then hybridized with WT2. The nuclear protein (6 µg) was mixed in
binding buffer (20 µL), which consisted of 20 mM
Tris-HCl, pH 8.0, 50 mM KCl, 0.5 mM EDTA, 15 mM MgCl2, 10% glycerol, 1 mM DTT, 2 µg of poly(dI-dC)-poly(dI-dC), and competitor
DNA as indicated in the figure legends. The unlabeled probe was used as
a wild-type competitor. For mutant competitor, the following
oligonucleotides with a 3-bp substitution were prepared and hybridized:
5
-GTCTGAGGcTTTTcCcGTAATAAAGAAACGA-3
(MT1) and 5
-TCGTTTCTTTATTACgGgAAAAgCCTCAGAC-3
(MT2). The mutated
nucleotides are indicated in lowercase. The reaction mixture was
preincubated for 5 min. Then, 10,000 cpm of the labeled DNA probe was
added to the reaction mixture. The binding reaction was continued for 15 min at 37°C. Samples were loaded onto a 5% polyacrylamide gel that contained 10% glycerol, 45 mM Tris-borate, and 1 mM EDTA (0.5× TBE buffer) and subjected to electrophoresis
at 4°C. The gel was dried and exposed overnight to an imaging plate
(Fuji Photo Film Co., Kanagawa, Japan). The image was visualized with a
Bio Imaging Analyzer (model BAS2000, Fuji).
 |
RESULTS |
Characterization of the Genomic Clone of the pra2
Gene and Determination of Its Transcriptional Start Site
The nucleotide sequence of the genomic clone of the
pra2 gene is shown in Figure
1. The gene contained two exons and one
intron. The deduced amino acid sequences agreed with those of cDNA
(Nagano et al., 1993
), except that Gly-206 was replaced by Ala. This
may be caused by the fact that the cDNA and genomic libraries were derived from different cultivars. The predicted protein sequences had
the conserved domains for GTP binding (Nagano et al., 1993
). Primer-extension analysis revealed that the transcriptional start site
was located 196 nucleotides upstream of the translational start site of
the pra2 gene (Fig. 1). The putative TATA box was located 24 bp upstream from this transcriptional start site. A characteristic
feature of the upstream sequence was the presence of a 113-bp inverted
repeat element (from
1226 to
1114), which displayed 88% sequence
similarity with the upstream region of one of the pea lipoxygenase
genes (lox1:Ps:2; Forster et al., 1994
). The PCR and Southern-blot
analyses showed that similar elements were dispersed throughout the
genome of pea plants (data not shown). These results showed that the
element is a family of interspersed DNA elements. Whereas the function
of most repetitive DNAs has not been elucidated, some of them have been
implicated in various cellular functions, such as the regulation of
gene expression (Bureau and Wessler, 1994
). However, this element is not involved in the light down-regulated expression as described below,
although further study is required to elucidate the role of this
element in the regulation of gene expression.

View larger version (94K):
[in this window]
[in a new window]
| Figure 1.
Nucleotide sequence of the pea pra2
gene. Nucleotides are numbered on the right side, with the
transcriptional start site designated +1. Amino acids are numbered on
the left side, with the first residue of the protein designated +1.
Arrowheads show exon-intron boundaries. The 113-bp inverted repeat
element is underlined. Arrows show inverted repeats. The location of
the 93-bp region is boxed.
|
|
Intact Epicotyls Were Necessary for This Transient Assay
pra2 mRNA and protein are mainly present in the growing
zone of etiolated pea seedlings and disappear upon exposure to light (Yoshida et al., 1993
; Nagano et al., 1995
). Because we wanted to
introduce a reporter gene into this zone, we examined whether it would
be possible to use a stem section of the growing zone. We examined
whether the pra2 protein in the stem section was stable for
12 h in darkness, as it is in intact seedlings. Immunoblot analysis using a monoclonal antibody against the pra2
protein indicated that the pra2 protein of intact seedlings
was found in darkness (Fig. 2a, lane 1)
and decreased after 12 h of white-light irradiation (lane 2). The
pra2 protein also decreased when the stem was cut and kept
in darkness for 12 h (lane 3). The results indicated that cutting
the stem caused some changes that affected pra2 protein
expression and that the stem section could not be used instead of
intact stems for our experiments. Therefore, we used intact seedlings
to examine reporter-gene expression in a transient assay. Bombardment
of the growing zone of intact seedlings with gold particles, which
might wound plants, did not affect the expression of the
pra2 protein (lane 4).

View larger version (18K):
[in this window]
[in a new window]
| Figure 2.
Determination of the experimental conditions. a,
Effect of cutting the stem on pra2 protein levels. Total
proteins from the stem (1.0 cm from the top of the hook) were
extracted, separated by SDS-PAGE, and probed with
anti-pra2 protein IgG. The same amount of protein (30 µg) was put in each lane. Six-day-old seedlings grown in darkness
(lane 1) were irradiated with white light for 12 h (lane 2). Stem
sections (1.0 cm from the top of the hook) of the 6-d-old seedlings
were cut and kept in darkness for 12 h on wet cotton (lane 3). The
growing zone of etiolated 6-d-old seedlings were bombarded with gold
particles and kept in darkness for 12 h (lane 4). b, Effect of
pra2 upstream fragment on the reporter-enzyme activity
in stems of intact plants and sections. The PL1 construct was
introduced into the growing zone of intact etiolated stem (left) or
stem section (1 cm from the top of the hook; right) by particle
bombardment with the 35S-GUS construct as the internal standard.
Reporter-enzyme activity was measured after 12 h of darkness (D)
or 12 h of white-light irradiation (L). Relative activity was
defined in "Materials and Methods," and the average of PL1 in
darkness was taken to be 100. Values are the means of at least four
independently bombarded samples with error bars representing
SE (n 4). c, Comparison of
reporter-gene expression in different parts of intact stem. PL1
construct was bombarded into the indicated parts, and the
reporter-enzyme activity was measured as described.
|
|
We fused the DNA sequence extending 2325 bp upstream from the
translational start site (196-bp 5
-untranslated region of mRNA and
2129-bp upstream region; Fig. 1) to the LUC reporter gene (PL1
construct; Fig. 3). Then, we introduced
the PL1 construct into the growing zone of intact, etiolated stem by
particle bombardment with the 35S-GUS construct as the internal
standard. When the relative activity of the reporter enzyme in darkness
was taken to be 100, the activity decreased to about 37 after 12 h
of illumination (Fig. 2b, left). When we bombarded the PL1 construct
into a cut section of growing zone, we did not observe light
down-regulated expression of the reporter enzyme (Fig. 2b, right).
These results indicated that the 2325-bp 5
-upstream region was
sufficient to down-regulate the expression of the LUC gene in the
growing zone of intact stem upon light irradiation.

View larger version (23K):
[in this window]
[in a new window]
| Figure 3.
5 -Deletion analysis of the
pra2 upstream region. The 5 -deletion constructs
containing the pra2 upstream region were fused to the
promoter-less pBI221-LUC+ plasmid. The numbers refer to the 5 end of
the pra2 upstream fragments from the transcriptional
start site in Figure 1. The names of the resulting plasmids are
indicated. Equivalent amounts of pBI221-LUC+ plasmid DNA fused to
different pra2 upstream regions were introduced into the
growing zone of etiolated pea stem by particle bombardment, with the
35S-GUS construct as the internal standard. After bombardment, samples
were kept in darkness (D) or under continuous white light (L) for
12 h. Relative activity is defined in Figure 2b. Values are the
means of at least four independently bombarded samples with error bars
representing SE (n 4). UTR,
Untranslated region; NOS, nopaline synthase terminator.
|
|
We also introduced the PL1 construct into different zones of intact,
etiolated pea stems (0-1, 1-2, and 2-3 cm from the top of the hook).
The region of 0 to 1 cm elongated about 2-fold within 12 h,
whereas 1- to 2- and 2- to 3-cm regions elongated little (data not
shown). The LUC activity in the growing zone was much higher than that
in the nongrowing zone (Fig. 2c). This result agreed with previous data
(Nagano et al., 1995
) and indicated that the 2325-bp region conferred
growing-zone-specific expression on the reporter gene. It is necessary
to introduce reporter-gene constructs into the growing zone to get
reliable data.
5
-Deletion Analyses Showed That the pra2 Upstream
Region Had a cis-Regulatory Region for Light
Down-Regulated Expression
To broadly determine the light down-regulated region, we carried
out the experiments using white light. Then we used red and far-red
lights to precisely determine the cis element involved in
phytochrome down-regulation. We constructed a series of 5
deletions of
the pra2 upstream region and fused them to the LUC reporter
gene, as shown in Figure 3. The resulting plasmids were bombarded into
the growing zone of etiolated, intact stems. We determined the
comparative expression of the reporter gene in darkness and after
12 h of white light (Fig. 3) for each of the deletion constructs.
Four constructs, PL1 to PL4, showed similar levels of activity in
darkness, and this activity was decreased by light. These findings
indicated that a region sufficient to confer higher expression in dark
than in light was present within the
734-bp region from the
transcriptional start site. However, in the PL5 to PL8 constructs the
activity in darkness decreased to about one-fifth of that of PL4,
although a little activity was recovered in PL7. In addition, the
effect of light on expression was almost abolished. This result
indicated a critical region for expression in darkness, and the
response to light was at least present in the 93-bp sequence from
734
to
642. The activity increase of the PL7 construct in darkness
suggested the possible presence of a repressing region from
593 to
292 and an activating region from
291 to
101.
The 93-bp Region Conferred Light Down-Regulated Expression to a
Heterologous Promoter
We performed gain-of-function 3
-deletion analysis to determine
whether this 93-bp region was able to confer light down-regulation to a
non-light-regulated heterologous promoter. We fused several 3
-deleted
fragments of the pra2 upstream region to the minimal CaMV
35S promoter (
90 from the transcriptional start site, designated as
35S90) and LUC reporter gene (Fig. 4). We
constructed five plasmids containing the 93-bp region, as shown in
Figure 4, and compared the light responsiveness of the reporter-gene
expression in each construct. In the absence of the pra2 5
region, the activity of the reporter gene did not change upon light
irradiation, and light down-regulation was not observed (Fig. 4,
control). The GF1 construct, from which the sequence between the
pra2's own TATA box and the translational start site (
24
to +196) was deleted, could not confer down-regulated expression of the
reporter gene. However, the further deleted construct (
101 to +196),
GF2, could confer expression. This suggests that the element, which is
located between
101 and
25, may interact with the as-1 sequence of
the CaMV 35S90 promoter. This interaction may determine the light response of the GF1 construct. The other 3
-deleted constructs, GF3,
GF4, and GF5, conferred down-regulation of the reporter gene. These
results indicated that the 93-bp region was sufficient to confer light
down-regulated expression to a heterologous promoter, 35S90. As shown
by the activity in light, the basal level decreased with the length of
the fused fragment (from GF1-GF4), suggesting that the length or
sequence affected expression at the basal level.

View larger version (21K):
[in this window]
[in a new window]
| Figure 4.
Gain-of-function analysis. A, CaMV 35S promoter of
90 bp from the transcriptional start site fused to the LUC reporter
gene was used as the control construct. To the control construct,
several 3 -deleted fragments of the pra2 upstream region
were fused. The names of the resulting plasmids are indicated on the
right. White bold line, 93-bp region; thin line, deleted region.
Control or GF1 to GF5 constructs were introduced into the growing zone
of etiolated, intact stem by particle bombardment, with the 35S-GUS
construct as the internal standard. After bombardments, the plants were
kept in darkness (D) or irradiated with white light (L) for 12 h.
Values are the means of at least four independently bombarded samples,
with error bars representing SE (n 4). Relative activity is defined in Figure 2b. NOS, Nopaline synthase
terminator.
|
|
The 24-bp Region Is Involved in Phytochrome Down-Regulated
Expression
pra2 expression is down-regulated by phytochrome
(Yoshida et al., 1993
). To investigate whether a cis element
involved in the down-regulation exists in the 93-bp region, we examined
the effect of a brief red-light irradiation on reporter-gene expression using the PL4 construct. After particle bombardment of the PL4 construct, the plants were irradiated with 2 min of red light and kept
for 12 h in darkness, and the reporter enzyme activity was then
measured. A brief red light repressed the reporter enzyme activity, and
this repression was reversed by far-red irradiation provided
immediately after red-light irradiation (Fig.
5, PL4). In the plants bombarded with the
PL5 construct lacking the 93-bp region, red-light irradiation did not
repress the reporter-enzyme activity (Fig. 5, PL5). These results
suggested that the 93-bp region was necessary for phytochrome
down-regulation.

View larger version (26K):
[in this window]
[in a new window]
| Figure 5.
Red/far-red reversibility of the change in the
reporter-enzyme activity. Different kinds of constructs containing the
pra2 upstream region were prepared as described in
``Materials and Methods''. The names of the resulting plasmids are
indicated on the right. White bold line, 93-bp region; thin line,
deleted region. Equivalent amounts of each plasmid were introduced into
5- or 6-d-old etiolated seedlings as described in ``Materials and Methods''. After bombardment, the plants were exposed to red light for
2 min (R) or far-red light for 5 min immediately after red light for 2 min (R/FR) and then were returned to darkness for 12 h. Dark and
far-red controls are indicated as D and F, respectively. Values are the
means of 5 to 11 independently bombarded samples, with error bars
representing SE. Relative activity is defined in Figure 2b.
A fine-scale figure of PL4C is shown in the inset. NOS, Nopaline
synthase terminator.
|
|
To examine whether the 93-bp region was sufficient to confer
phytochrome down-regulation to its own minimal promoter, we fused the
93-bp fragment to its own TATA box and 5
-untranslated region (Fig. 5,
PL4C). We observed red-light-inducible and far-red-light-reversible repression, although the basal expression was reduced (Fig. 5, PL4C).
These results indicated that the 93-bp region was sufficient to confer
phytochrome down-regulation.
For further analysis, we deleted 62 bp of the 93-bp region in PL4 and
measured its activity (Fig. 5, PL4A). We observed red-light-inducible and far-red-light-reversible repression for PL4A containing 31 bp of
the 93-bp region. The reduction of the expression in PL4A implies an
involvement of the 62-bp region in basal expression. The internal
deletion of 24 bp (
666 to
643) in the 31-bp region abolished
red-light-regulated repression (Fig. 5, PL4B). These results indicated
that the 24-bp region from
666 to
643 was responsive to phytochrome
down-regulated expression and that the 62-bp region from
734 to
673
affected the basal expression level. The level of PL4B activity was
almost the same as that of red-light-treated plants in PL4, and the
deletion of 24 bp from PL4 did not decrease the expression of basal
level. However, the deletion decreased the expression in darkness (Fig.
5, PL4B). These results suggested that the 24-bp region was involved in
enhanced expression in darkness.
LS Revealed That the 12-bp Element Mediated Phytochrome
Down-Regulated Expression
To identify the cis element necessary for
phytochrome down-regulation, we conducted LS analysis. We prepared five
constructs with 6-bp mutations in the 31-bp region of the PL4A
construct (Fig. 5), as shown in Figure 6.
The 6-bp mutations correspond to the PstI recognition
sequence. We examined the effect of red light on expression using the
resulting plasmids. LS2 and LS3 did not show red-light down-regulation
(Fig. 6). In particular, the red-light repression was completely
abolished in the LS3 construct, suggesting that the core region was
located in the mutated region within LS3. The other three constructs,
LS1, LS2, and LS5, retained the red-light repression. These results
indicated that the phytochrome down-regulation was mediated by the
element within the 12-bp region, the sequence of which was
GGATTTTACAGT. This element did not show any sequence similarity with
the previously reported elements involved in phytochrome- or
light-regulated expression.

View larger version (39K):
[in this window]
[in a new window]
| Figure 6.
LS analysis to define the 12-bp phytochrome
down-regulated element. LS constructs in the pra2
5 -upstream region are shown. The positions of mutated nucleotides are
indicated in lowercase and underlined. The WT sequence corresponds to
the PL4A construct in Figure 5. The 12-bp phytochrome-responsive
element is boxed. Equivalent amounts of each plasmid were introduced
into 5- or 6-d-old etiolated seedlings as described. After bombardment,
the plants were exposed to red light for 2 min (R) and then returned to
darkness for 12 h. D, Dark control. Values are the means of at
least five independently bombarded samples, with error bars
representing SE. Relative activity is defined in Figure
2b.
|
|
A Nuclear Factor Specifically Bound to the 12-bp Element in
Vitro
To examine the presence of nuclear factors such as DNA-binding
proteins bound to the 12-bp element specifically, we conducted gel-retardation assays using nuclear extracts from pea epicotyls. As a
probe, we prepared a 31-bp synthetic oligonucleotide containing the
sequence from
672 to
642 (WT; Fig.
7a). Addition of the nuclear extracts
from both etiolated and light-irradiated (6 h) pea plants to the
binding reaction mixture showed the retarded band of the DNA-protein
complex (Fig. 7b, lanes 2 and 3). The signal of etiolated plants was
stronger than that of light-irradiated plants (lanes 2 and 3),
suggesting that the amount of this nuclear factor was higher in the
dark-grown epicotyls than in the light-irradiated plants. This
dark-light difference was observed in three independent extracts. To
test whether the observed binding was specific to the 12-bp element, we
prepared an oligonucleotide in which the adenines in the 12-bp element
were changed to cytosines (MT; Fig. 7a). The band was diminished by
50-fold WT competitor (lanes 4 and 5) but not by MT competitor (lanes 6 and 7). MT competitors in 200- or 400-fold excess could not compete
with labeled probe (lanes 8 and 9). These data indicated that the
observed band was a complex of probe DNA and nuclear factor
specifically bound to the 12-bp element.

View larger version (34K):
[in this window]
[in a new window]
| Figure 7.
Gel-mobility shift assays with the synthetic
oligonucleotides. a, Sequences of synthetic oligonucleotides used in
this experiment are shown. The 12-bp sequence is boxed. Nucleotides in
the MT oligonucleotide that are different from the WT oligonucleotide
are indicated in lowercase with arrows. b, Binding of nuclear proteins
from pea stems to the WT oligonucleotide and competition with the WT
and MT oligonucleotides. The 12-bp-specific bound complex is indicated
by the arrow. D and L indicate the nuclear extracts of dark-grown
plants and plants exposed to light for 6 h, respectively.
|
|
 |
DISCUSSION |
We present evidence that the pra2 upstream fragment of
2325 bp from the initiation codon can direct a reporter gene to be expressed at a higher level in darkness than in light in the growing zone of etiolated pea stem. In developing a transient assay system, we
found that cutting the stem drastically decreased the pra2 protein level and reporter-gene expression. The expression of the
reporter gene by our transient assay was analogous to that of the
pra2 gene itself (Yoshida et al., 1993
; Nagano et al., 1995
). This suggests that the experimental system is a reliable way to
examine pra2 expression. By 5
-deletion analysis of the pra2 upstream region (Fig. 3), we showed that 93 bp from
734 to
642 could drive light down-regulated expression of the LUC gene. The 93-bp region conferred the down-regulation to a heterologous CaMV 35S90 promoter (Fig. 4). The 93-bp region was sufficient to confer
phytochrome down-regulation of the reporter gene when combined with its
own TATA box and 5
-untranslated region (Fig. 5). Furthermore, we
discovered that a 12-bp element within the 93-bp region mediated
phytochrome down-regulated expression (Fig. 6). We also discovered that
nuclear factor bound to this element in a light-dependent manner (Fig.
7).
To our knowledge, 5
regions of the genes down-regulated by phytochrome
have been characterized for PHYA (Bruce et al., 1991
), NPR (Okubara et al., 1993
; Williams et al., 1994
),
AS1 (Nagi et al., 1997
; Neuhaus et al., 1997
), and
TubB1 (Tonoike et al., 1994
). The elements containing the
TGGG sequence were shown to be involved in down-regulation by
phytochrome for PHYA (Bruce et al., 1991
) and AS1
(Neuhaus et al., 1997
). However, in the case of NPR1, two
elements that were necessary for both phytochrome- and ABA-mediated expression of this gene were identified, and these elements did not
contain the TGGG sequence (Weatherwax et al., 1998
). Rather, phytochrome regulated ABA levels, and then ABA affected the
NPR1 expression. Thus, the mechanism of down-regulation of
this gene is quite different from that of other genes such as
PHYA and AS1. In the pra2 gene the
12-bp GGATTTTACAGT element mediates down-regulation by phytochrome.
This element is similar to the
300 element that is involved in
endosperm-specific expression of the high-Mr
glutenin gene (Colot et al., 1987
; Thomas and Flavell, 1990
), but the
12-bp element is functionally different from the
300 element.
Moreover, the putative core sequence of the 12-bp element TACAGT (LS3
mutated position) does not contain the same motif reported previously. The mechanism of phytochrome down-regulation of the pra2
gene is probably different from that of other genes characterized
previously.
It is well known that the promoter context affects the light response
when cis elements are fused to heterologous promoters (Puente et al., 1996
). In the CaMV 35S90 promoter, an activator sequence, as-1, affects light response interacting with a fused fragment (Terzaghi and Cashmore, 1995
). The data in Figure 4 suggest that the 93-bp region could confer light down-regulation to a 35S90
promoter. The sequence from
101 to
25 of the 5
-upstream region of
pra2 did not confer the light response to the 35S90 promoter. These results suggest that the interaction between the regions from
101 to
25 and as-1 suppressed the light
down-regulation.
The binding manner of nuclear protein to the 12-bp element also showed
an interesting feature. Apparently, the amount of protein bound to this
element decreased upon light irradiation (Fig. 7b), suggesting an
involvement of this protein in light down-regulation. Here we propose
one simple hypothesis: The protein bound to the 12-bp element enhances
transcription of pra2 in darkness, and its dissociation from
the 12-bp region upon light irradiation results in repression of the
transcription. In the case of PHYA, the putative
trans factor RF1 is thought to bind RE1 when irradiated and
regulate gene repression. The 12-bp binding factor may be a new type of
DNA-binding protein involved in down-regulation by phytochrome.
Molecular cloning and characterization of this trans factor
may reveal the mechanism of phytochrome signal transduction.
We also demonstrated that the pra2 5
-upstream region was
involved in the growing-zone-specific expression of the reporter gene
in etiolated pea stem. To our knowledge, expression of the
-tubulin
TUB1 (or soybean tubB1) gene is similar to that
of pra2. These two genes are specifically expressed in
etiolated stems (Han et al., 1991
; Nagano et al., 1995
). Previously,
Tonoike et al. (1994)
demonstrated that a 2-kb fragment 5
upstream of
the tubB1 gene was sufficient to direct hypocotyl expression
and light down-regulation. Both phytochrome A and phytochrome B
regulate the TUB1 gene. However, TUB1 expression
is reduced by red light but is not reversed by far-red light (Leu et
al., 1995
). Stem elongation is inhibited by a brief red-light
irradiation, and this effect was reversed by subsequent exposure to
far-red light. The pra2 gene possibly plays an important
role in the morphogenesis of etiolated seedlings and the inhibition of
stem elongation by light.
 |
FOOTNOTES |
1
This work was supported by grants from the
Japanese Ministry of Education, Science, Sports and Culture and from
the Japan Society for the Promotion of Science (Research for the Future Program, no. JSPS-RTFT.96L006012). T.I. received Research Fellowships from the Japan Society for the Promotion of Science for Young Scientists.
*
Corresponding author; e-mail sasaki{at}agr.nagoya-u.ac.jp; fax
81-52-789-4296.
Received December 1, 1998;
accepted March 4, 1999.
 |
ABBREVIATIONS |
Abbreviations:
CaMV, cauliflower mosaic virus.
LS, linker-scanning.
LUC, luciferase.
 |
ACKNOWLEDGMENTS |
We thank Drs. H. Mori, K. Yoshida, K. Nakamura, K. Maeo, and S. Shimizu for their technical advice. We also thank Dr. A.T. Jagendorf
for discussion. The pBI221-LUC+ plasmid was a kind gift of Dr. Kazuyuki
Hiratsuka.
 |
LITERATURE CITED |
Bruce WB,
Deng X-W,
Quail PH
(1991)
A negatively acting DNA sequence element mediates phytochrome-directed repression of phyA gene transcription.
EMBO J
10:
3015-3024
[ISI][Medline]
Bureau TE,
Wessler SR
(1994)
Stowaway: a new family of inverted repeat elements associated with the genes of both monocotyledonous and dicotyledonous plants.
Plant Cell
6:
907-916
[Abstract]
Carabelli M,
Morelli G,
Whitelam G,
Ruberti I
(1996)
Twilight-zone and canopy shade induction of the Athb-2 homeobox gene in green plants.
Proc Natl Acad Sci USA
93:
3530-3535
[Abstract/Free Full Text]
Colot V,
Robert LS,
Kavanagh TA,
Bevan MW,
Thompson RD
(1987)
Location of sequences in wheat endosperm protein genes which confer tissue-specific expression in tobacco.
EMBO J
6:
3559-3564
[ISI][Medline]
Forster C,
Knox M,
Domoney C,
Casey R
(1994)
lox1:Ps:2, a Pisum sativum seed lipoxygenase gene.
Plant Physiol
106:
1227-1228
[Medline]
Han I-S,
Jongewaard I,
Fosket DE
(1991)
Limited expression of a diverged
-tubulin gene during soybean (Glycine max [L.] Merr.) development.
Plant Mol Biol
16:
225-234
[Medline]
Ishiguro S,
Nakamura K
(1992)
The nuclear factor SP8BF binds to the 5
-upstream regions of three different genes coding for major proteins of sweet potato tuberous roots.
Plant Mol Biol
18:
997-1008
[CrossRef][ISI][Medline]
Jefferson RA,
Kavanaugh TA,
Bevan MW
(1987)
GUS fusions:
-glucuronidase as a sensitive and versatile gene fusion marker in higher plants.
EMBO J
6:
3901-3907
[ISI][Medline]
Kehoe DM,
Degenhardt J,
Winicov I,
Tobin EM
(1994)
Two 10-bp regions are critical for phytochrome regulation of a Lemna gibba Lhcb gene promoter.
Plant Cell
6:
1123-1134
[Abstract]
Kosugi S,
Ohashi Y,
Nakajima K,
Arai Y
(1990)
An improved assay for
-glucuronidase in transformed cells: methanol almost completely suppresses a putative endogenous
-glucuronidase activity.
Plant Sci
70:
133-140
[CrossRef]
Leu W-M,
Cao X-L,
Wilson TJ,
Snustad DP,
Chua N-H
(1995)
Phytochrome A and phytochrome B mediate the hypocotyl-specific downregulation of TUB1 by light in Arabidopsis.
Plant Cell
7:
2187-2196
[Abstract]
Miller AJ,
Short SR,
Hiratsuka K,
Chua N-H,
Kay SA
(1992)
Firefly luciferase as a reporter of regulated gene expression in higher plants.
Plant Mol Biol Rep
10:
324-337
Nagano Y,
Matsuno R,
Sasaki Y
(1991)
Sequence and transcriptional analysis of the gene cluster trnQ-zfpA-psaI-ORF231-petA in pea chloroplasts.
Curr Genet
20:
431-436
[CrossRef][ISI][Medline]
Nagano Y,
Murai N,
Matsuno R,
Sasaki Y
(1993)
Isolation and characterization of cDNAs that encode eleven small GTP-binding proteins from Pisum sativum.
Plant Cell Physiol
34:
447-455
[Abstract/Free Full Text]
Nagano Y,
Okada Y,
Narita H,
Asaka Y,
Sasaki Y
(1995)
Location of light-repressible, small GTP-binding protein of the YPT/rab family in the growing zone of etiolated pea stems.
Proc Natl Acad Sci USA
92:
6314-6318
[Abstract/Free Full Text]
Nagi N,
Tsai F-Y,
Coruzzi G
(1997)
Light-induced transcriptional repression of the pea AS1 gene: identification of cis-elements and trans-factors.
Plant J
12:
1021-1034
[CrossRef][ISI][Medline]
Neuhaus G,
Bowler C,
Hiratsuka K,
Yamagata H,
Chua N-H
(1997)
Phytochrome-regulated repression of gene expression requires calcium and cGMP.
EMBO J
16:
2254-2264
Okubara PA,
Williams SA,
Doxsee RA,
Tobin EM
(1993)
Analysis of genes negatively regulated by phytochrome action in Lemna gibba and identification of a promoter region required for phytochrome responsiveness.
Plant Physiol
101:
915-924
[Abstract]
Puente P,
Wei N,
Deng X-W
(1996)
Combinatorial interplay of promoter elements constitutes the minimal determinants for light and developmental control of gene expression in Arabidopsis.
EMBO J
15:
3732-3743
[ISI][Medline]
Sasaki Y,
Sakihama T,
Kamikubo T,
Shinozaki K
(1983)
Phytochrome-mediated regulation of two mRNAs, encoded by nuclei and chloroplasts of ribulose-1,5-bisphosphate carboxylase/oxygenase.
Eur J Biochem
133:
617-620
[ISI][Medline]
Shimizu S,
Itoh Y,
Yamazaki K
(1996)
Temperature-dependent increase in the DNA-binding activity of a heat shock factor in an extract of tobacco cultured cells.
Plant Mol Biol
31:
13-22
[CrossRef][ISI][Medline]
Takeuchi Y,
Dotson M,
Keen NT
(1992)
Plant transformation: a simple bombardment device based on flowing helium.
Plant Mol Biol
18:
835-839
[CrossRef][Medline]
Terzaghi WB,
Cashmore AR
(1995)
Light-regulated transcription.
Annu Rev Plant Physiol Plant Mol Biol
46:
445-474
[CrossRef][ISI]
Thomas MS,
Flavell RB
(1990)
Identification of an enhancer element for the endosperm-specific expression of high molecular weight glutenin.
Plant Cell
2:
1171-1180
[Abstract/Free Full Text]
Tonoike H,
Han I-S,
Jongewaard I,
Doyle M,
Guiltinan M,
Fosket DE
(1994)
Hypocotyl expression and light downregulation of the soybean tubulin gene, tubB1.
Plant J
5:
343-351
[Medline]
Weatherwax SC,
Williams SA,
Tingay S,
Tobin EM
(1998)
The phytochrome response of the Lemna gibba NPR1 gene is mediated primarily through changes in abscisic acid levels.
Plant Physiol
116:
1299-1305
[Abstract/Free Full Text]
Williams SA,
Weatherwax SC,
Bray EA,
Tobin EM
(1994)
NPR genes, which are negatively regulated by phytochrome action in Lemna gibba L. G-3, can also be positively regulated by abscisic acid.
Plant Physiol
105:
949-954
[Abstract]
Yoshida K,
Nagano Y,
Murai N,
Sasaki Y
(1993)
Phytochrome-regulated expression of the genes encoding the small GTP-binding proteins in peas.
Proc Natl Acad Sci USA
90:
6636-6640
[Abstract/Free Full Text]