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Volume 270,
Number 5,
Issue of February 3, 1995 pp. 2403-2410
©1995 by The American Society for Biochemistry and Molecular Biology, Inc.
Analysis
of the Chicken GPAT/AIRC Bidirectional Promoter for de
Novo Purine Nucleotide Synthesis (*)
(Received for publication, September 7, 1994; and in revised form, October 20, 1994)
Anthony
Gavalas (§), ,
Howard
Zalkin (¶)
From the Department of Biochemistry, Purdue University, West
Lafayette, Indiana 47907
ABSTRACT
INTRODUCTION
MATERIALS AND METHODS
RESULTS
DISCUSSION
FOOTNOTES
ACKNOWLEDGEMENTS
REFERENCES
ABSTRACT
GPAT and AIRC encode two enzymes that catalyze
steps 1 and 6 plus 7, respectively, of the de novo purine
biosynthetic pathway. The chicken genes are closely linked and
divergently transcribed from an 230-base pair intergenic region.
The promoter was scanned by deletion mutagenesis in a bireporter vector
that allowed assay of transcriptional activity in both directions in
transfected HepG2 and chicken LMH cells. Three classes of deletions
were obtained: those affecting bidirectional transcription, those
predominantly affecting GPAT transcription, and those
predominantly affecting AIRC transcription. Defects in
bidirectional transcription resulted from removal of an initiator-like
element overlapping the AIRC transcription start site, as well
as deletions removing a series of GC and CCAAT boxes from the AIRC proximal half of the promoter and a CCAAT-containing segment from
the GPAT side. Several regions in the GPAT proximal
half of the promoter, including an octamer-like motif downstream from
the transcription start site, were required predominantly for GPAT expression. Evidence for interaction of HeLa nuclear proteins with
some of these sites was obtained by gel retardation, DNase I, and
methylation interference assays. Overall, the results showed that the
intergenic region is an integrated bidirectional promoter and that a
novel initiator-like element plays a central role in coordinating
expression of the divergently transcribed AIRC and GPAT genes.
INTRODUCTION
De novo biosynthesis of purine nucleotides proceeds by
a 14-step branched pathway via IMP. GPAT-encoded glutamine
5`phosphoribosylpyrophosphate amidotransferase catalyzes the first
committed step of the pathway, and 5`-phosphoribosylaminoimidazole
carboxylase/5`-phosphoribosyl
4-(N-succinocarboxamide)-5-aminoimidazole synthetase, encoded
by AIRC, catalyzes steps 6 and 7. The approximate chromosomal
locations of the seven human genes required for AMP synthesis were
deduced by complementing Chinese hamster ovary mutants deficient in AMP
synthesis and by subsequent cytogenetic analysis of Chinese hamster
ovary-human somatic cell hybrids. GPAT and AIRC were
thus mapped to overlapping regions of chromosome 4, whereas other genes
of the pathway were localized on different chromosomes (Barton et
al., 1991). More recently, the human GPAT-AIRC locus has
been mapped by in situ fluorescence hybridization to the q12
region of chromosome 4 (Brayton et al., 1994). In order to
set the groundwork for investigations of gene expression and regulation
of this pathway in vertebrates, we recently cloned and characterized
the chicken and human GPAT genes and the proximal AIRC genes (Brayton et al., 1994; Gavalas et al.,
1993). This work established that GPAT and AIRC are
closely linked and divergently transcribed from intergenic regions of
approximately 230 and 625 bp ( )in chickens and humans,
respectively. Intron/exon boundaries are strictly conserved, as is the
approximate size of the GPAT gene. On the other hand, human AIRC is approximately 2-fold larger than the corresponding
chicken gene. The two promoters have also diverged significantly,
although the close linkage of the two genes has been retained along
with a high GC content and the presence of several Sp1 boxes. Both
promoters lack TATA elements. Although the functional consequences of
tight linkage between GPAT and AIRC are not known,
promoters with the capacity to direct bidirectional transcription may
provide one mechanism for the co-regulation of functionally related
genes. As such, this arrangement may constitute the eukaryotic
equivalent of a prokaryotic operon. This structural unit was named a
dioskourion (from the Greek Dioskouri, the mythological inseparable
twin sons of Zeus) (Gavalas et al., 1993). Bidirectional
promoters may also be useful as a genetic engineering tool, directing
expression of two genes in predetermined relative amounts and/or in a
tissue-specific manner. Previous experiments (Gavalas et
al., 1993) have shown that chicken GPAT-AIRC promoter
strength was about 10-fold higher in the AIRC direction
compared with the GPAT direction using a bireporter promoter
vector in transfected HepG2 cells. In addition, the intergenic region
was dissected to yield ``half-promoters'' having about 30%
function in the GPAT direction and 80% function in the AIRC direction. In this earlier work, a bidirectional promoter
was defined operationally as a short segment of DNA that initiates
bidirectional transcription in vivo. The question remains,
however, whether common cis-elements and assembled
transcription factors are used for transcription in both directions, as
in an ``authentic'' bidirectional promoter or whether
expression in the two directions employs distinct cis-elements. The latter case could result from juxtaposition
of separate promoters. In order to identify cis-acting sites
and to distinguish between the two types of promoter function, deletion
mutants were constructed and tested for transcriptional activity by
transfection of a bireporter vector carrying the LUC and CAT genes in divergent orientations. Two hepatoma cell lines,
human HepG2 and chicken LMH, were used to evaluate the effect of these
deletions. cis-Elements were found for bidirectional
expression in both cell lines. One of these cis-elements,
central for the expression of both genes, is a novel initiator
(Inr)-like element, situated around the AIRC transcription
start site. Mobility shift, DNase I, and methylation interference
assays limited this element to 41 bp, showed that nuclear protein
binding results in hypersensitivity to DNase I at the AIRC transcription start site, and identified nucleotides involved in
specific DNA/protein contacts. cis-Elements also exist that
are largely side-specific, most notable of which is an octamer-like
motif found downstream from the GPAT transcription start site.
MATERIALS AND METHODS
Construction of Plasmids and Promoter
MutationsThe plasmid pSKP-R01 (Gavalas et al., 1993)
was used to introduce SmaI sites by site-directed mutagenesis
(Kunkel, 1985) in the positions depicted in Fig. 1and Fig. 7, resulting in plasmids pSma-0 to pSma-9. In this
nomenclature, the suffix (0-9) indicates the position of the SmaI site. SmaI/BamHI digestion of these
plasmids generates two fragments. The large fragment represents the
vector carrying a portion of the promoter, and the small one represents
the rest of the promoter. By combining small and large parts of
different plasmids, the mutations shown in Fig. 1were
generated. The positions of the SmaI sites are used to
designate regions deleted in a plasmid. Plasmid pSma-2.7i was
constructed by introducing SmaI sites at positions 2 and 7,
digesting the resulting double mutant with SmaI, religating,
and screening by restriction mapping for plasmids carrying the region
2-7 in the inverted orientation with respect to the starting
plasmid. All of the mutations were sequenced by the dideoxy sequencing
method (Sanger et al., 1977) using single-stranded phagemid
DNA and a primer that annealed to the part of the CAT gene
present in these plasmids.
Figure 1:
Map of promoter deletions. A,
the plasmid pSK-PRO1 was used for initial construction before
subcloning the mutated promoters into the bireporter plasmid
pLUC/CAT-3. The middle box between HindIII and SalI represents the promoter. The hatched parts correspond to the 5`-untranslated regions of the two genes that
were incorporated into the promoter. The LUC and CAT boxes represent 5` parts of these genes that are incorporated into this
plasmid. The line between the promoter and the reporter boxes
represents short polylinker sequences. B, schematic
representation of the promoter. Consensus sites for cis-elements and an octamer-like sequence are shown. The lowercase letter indicates a base deviating from the
consensus. Arrows denote the transcription start sites, and arrowheads indicate the positions of SmaI sites that
were introduced by site-directed mutagenesis. The exact sequence of
this region and the exact position of the SmaI sites are shown
in Fig. 7. WT, wild type. C, schematic
representation of the promoter mutations. The deletions are noted by
the interrupted line and the number of deleted bp is written in the
gap. Mutant 2.7i bears no deletion; instead, the region between points
2 and 7 is inverted. Constructs are named according to the region
deleted.
Figure 7:
Nucleotide sequence of the AIRC/GPAT bidirectional promoter. Flanking sites for HindIII at the
5` end and SalI at the 3` end that are used for subcloning are
not shown. Arrowheads indicate the positions of SmaI
sites used for construction of deletions. Potential GC and CCAAT
elements are boxed. Large bent arrows and filled
squares represent the transcription start sites as determined from
transient transfection experiments and endogenous mRNA, respectively.
The lowercase sequence at positions 50-90 contains the AIRC Inr-like element, the upward vertical arrow shows the position of the DNase I-hypersensitive site on the
bottom (noncoding) strand, and asterisks mark the interfering
nucleotides on the top strand (above the sequence) and the
bottom strand (below the sequence). Half-arrows above
the Inr-like element indicate the presence of an imperfect palindrome
with a 3-bp spacer. A region similar to the adenovirus major late
promoter Inr is noted at positions 43-55. Direct (underlined) repeats close to the GPAT transcriptional start sites are noted by Roman numerals.
An octamer-like motif is shown with lowercase letters at
positions 320-327, and its DNase I footprint is shown by solid lines above (top strand) and below (bottom
strand) the sequence.
The resulting mutagenized promoters were
subcloned as HindIII/SalI restriction fragments into
the bireporter plasmid pLUC/CAT-3. This plasmid is identical to the
plasmid pLUC/CAT-1 that was used earlier (Gavalas et al.,
1993) with the exception that the contiguous BamHI and SacI sites at the 3` end of the chloramphenicol
acetyltransferase (CAT) reporter have been replaced by a ClaI
restriction site. The resulting plasmids were checked by restriction
mapping and were purified through two cesium chloride gradient
ultracentrifugations in preparation for the transient transfection
assays.
Transient Transfections and Reporter AssaysHepG2
cells were grown in Eagle's minimal essential medium supplemented
with 10% fetal bovine serum at 37 °C with 5% CO to
60-80% confluency in 35-mm plates. LMH cells were grown in
Waymouth medium supplemented with 10% fetal bovine serum in 5% CO at 37 °C. HepG2 cells were transfected by the lipofection
method (Felgner et al., 1987) or by the calcium phosphate
(Ausubel et al., 1987) method, whereas LMH cells were
transfected only by the calcium phosphate procedure. Transfected cells
were incubated with 10% serum-supplemented medium for 24-48 h.
After removal from the plate, two-thirds of the cells were used to
prepare extract for the CAT assay (Seed and Sheen, 1988), and one-third
was used for preparation of extract for -galactosidase and
luciferase (LUC) assays. LUC and -galactosidase activities were
determined by chemiluminescent assays as described by the suppliers of
the reagents (Promega and Tropix). The light emission was measured
using a Monolight 2010 instrument (Analytical Luminescence Laboratory)
as relative light units. Protein concentration was determined by the
Bradford assay (Bradford, 1976), and CAT and LUC specific activities
were normalized for -galactosidase specific activity, derived from
transfection with an RSV-lacZ plasmid (Darn et al.,
1987). Plasmid pLUC/CAT-3 was used to obtain the background values of
the reporter assays.
Gel Retardation and Competition Assays for Protein-DNA
BindingProbes containing promoter regions were isolated from
plasmids pSma-2 and pSma-7 using the appropriate enzymes. Digestion of
pSma-2 with HindIII/XmaI (XmaI is a SmaI isoschizomer) and XmaI/AvaI gave the
probes that encompass regions between SmaI sites 0-2 and
2-4, designated 0.2 and 2.4, respectively. The AvaI site
is located at position 188 in Fig. 7. Digestion of pSma-7 with AvaI/XmaI and XmaI/SalI gave the
probes encompassing regions 5.7 and 7.9, respectively. After the first
cut, the end was dephosphorylated and labeled using T4 polynucleotide
kinase and [ - P]ATP. Then digestion with the
second restriction enzyme released the P-labeled fragment
of interest, which was isolated by polyacrylamide gel electrophoresis
and electroelution. Probe 79 (see Fig. 3) was prepared by the
polymerase chain reaction using end-labeled primers.
Figure 3:
Analysis of protein binding to the AIRC Inr region by gel retardation. A, protein-DNA
complexes with promoter probe fragment shown in C. The probe
was isolated from plasmid pSma-2 by digestion with HindIII and XmaI, sites that flank the sequence shown, and was end-labeled
with [ - P]ATP. Arrows identify two
specific protein-DNA complexes. These complexes were competed by Sp1
oligonucleotide and by segments of the promoter proximal to the AIRC transcription start site defined in C. Plasmid
pBluescript polylinker (169 bp) was the nonspecific competitor. All
competitors were used at a 100-fold molar excess. Noncompeted unmarked
bands may be nonspecific. B, protein-DNA complexes with probe PCR #79 (see C). This probe has 5` and 3` ends
corresponding to probes PCR #7 and PCR #9,
respectively. An arrow marks the position of a protein-DNA
complex competed by the unlabeled probe. The molar excess concentration
of the competitor is given. The nonspecific competitor (100-fold molar
excess) is the same as in A. C, the sequence of the
promoter around the AIRC transcription start site is shown.
The arrow and the filled square represent the
transcription start site determined by transient transfections and
endogenous mRNA, respectively. Arrowheads mark the positions
where SmaI sites were introduced and, therefore, the end
points of deletion mutations. The large box indicates the
minimal sequence around the transcription start site that competes for
the low mobility specific complex, and the small box indicates
the Sp1 site. The box with the dotted line represents
the homology with the adenovirus major late promoter Inr (see also Fig. 7). The open bars represent DNA fragments used as
competitors. PCR #1 is the same as the sequence
shown.
Typical
protein-DNA binding reactions of 20 µl contained 5 µg of HeLa
nuclear extract (Promega), 1 µg of
poly(dI dC)-poly(dI dC) (Boehringer Mannheim), 25 mM HEPES, pH 7.6, 50 mM KCl, 0.1 mM EDTA, 5 mM MgCl , 10% glycerol, 1 mM dithiothreitol, and
0.1% Nonidet P-40. Incubation was for 25 min at room temperature.
Subsequently, 20-25 fmol of labeled probe were added, and the
reaction was incubated for an additional 25 min at room temperature.
Protein-DNA complexes were resolved by electrophoresis on a 4% native
polyacrylamide gel. Competitor DNAs were prepared either by restriction
digestion or PCR and were preincubated, before the addition of the
labeled probe, in the binding reaction. Commercially available duplex
oligonucleotides (Promega) were also used as competitors: Sp1,
5`-ATTCGATCGGGGCGGGGCGAGC-3`; TFIID, 5`-GCAGAGCATATAAGGTGAGG TAGGA-3`;
OCT1, 5`-TGTCGAATGCAAATCACTAGAA-3`; CTF/NF1, 5`-CCTTTGGCATGCTGCCAATATG.
Polymerase Chain ReactionDue to a high GC
content, PCR through the GPAT/AIRC promoter region tends to
give mostly nonspecific amplified fragments and/or a very low yield of
the correct fragment. In order to optimize these reactions, we used the
Stratagene Opti-Prime PCR optimization kit. Buffers 6 and 10 (10 mM Tris HCl, pH 8.8 and 9.2, respectively, 1.5 mM MgCl , and 75 mM KCl) were found to give only
specific bands for the PCR fragments depicted in Fig. 3.
DNase I and Methylation Interference AssaysFor
the GPAT side of the promoter, DNase I footprints were carried
out using 50 or 100 µg of HeLa nuclear extract and scaling up the
binding reaction 5 and 10 times, respectively, with the exception of
the probe, which stayed the same. Probes were derived from pSma-7 by XmaI/SalI digestion and were labeled on either
strand. For the free DNA control, bovine serum albumin replaced HeLa
extract. For the AIRC Inr footprint, the binding reaction was
scaled up 5-fold. Probes were derived from pSma-2 by HindIII/XmaI digestion and were labeled on either
strand. After incubation, a reaction containing 100-125 fmol of
probe was digested with 3 units of DNase I for 1 min, and the reactions
were electrophoresed on a 4% polyacrylamide preparative gel. The gel
was exposed to film overnight at 4 °C; then the shifted band was
cut out, and the DNA was eluted on DEAE ion exchange membrane
(Schleicher and Schuell). Samples were run on a 10% polyacrylamide
sequencing gel, and the gel was exposed at -80 °C with an
intensifier screen for up to 4 days.For the AIRC Inr
methylation interference assays, the probes used above were methylated
(Ausubel et al., 1987). A 5-fold scaled-up binding reaction
was performed with HeLa extract and was electrophoresed on a 4%
acrylamide preparative gel. The gel was exposed at 4 °C, and then
the bands representing the complex and the free probe were recovered.
DNA was eluted and cleaved with piperidine to yield the G ladder
(Ausubel et al., 1987). Samples were run on a 10%
polyacrylamide sequencing gel, and the gel was exposed at -80
°C for up to 4 days.
RESULTS
Construction and in Vivo Expression of Mutant
PromotersDeletion mutations were designed in such a way that
their end points would encompass possible regulatory elements that were
inferred by visual inspection of the promoter sequence. The presence of
precise transcriptional start sites for both genes suggests the
existence of elements that are able to direct the basal transcriptional
apparatus to the correct place of transcription initiation. Deletions
were constructed by introducing SmaI sites into the promoter
positions shown in Fig. 1(A and B; and in
more detail in Fig. 7). By combining various SmaI/BamHI fragments, the deletions obtained in Fig. 1C were obtained. Use of the bireporter vector
facilitated analysis of the effect that such deletions have on both
sides of the promoter. Transient transfection assays in human and avian
cells revealed the presence of elements that positively affect
transcription on both sides. Results for assays of LUC and CAT
reporters to monitor transcription of AIRC and GPAT,
respectively, are given in Fig. 2. The mutations fall into three
classes: those that remove elements required for bidirectional
transcription and those that affect transcription predominantly in one
direction, either GPAT or AIRC. These deletions and
the further analysis of cis-elements are examined in the
sections that follow.
Figure 2:
Transcriptional activity of mutant
promoters. The activities of the mutant promoters in HepG2 and LMH
cells are expressed as the percentage of the wild type and are
represented by solid bars. Values are the average of at least
five independent transfections with standard deviations shown as error bars.
A Novel Element Around the AIRC Transcription Start Site
Required for Bidirectional TranscriptionA site in region 1.2
close to the position for AIRC transcription initiation is one
of the important cis-elements for bidirectional promoter
function. Expression from the AIRC and GPAT directions was reduced to less than 10 and 30% of wild type level,
respectively, in HepG2 cells in promoter deletion 1.2 (Fig. 2).
The defect in bidirectional expression of this promoter deletion was
comparable in LMH cells. To further define the functional site(s) and
to search for proteins that interact with the segment of the promoter
that flanks the AIRC transcription start site, electrophoretic
mobility shift assays were carried out using HeLa cell nuclear extract
and a DNA probe containing the 0-2 portion of the promoter. The
nucleotide sequence of the DNA probe is given in Fig. 3C. Two specific protein-DNA complexes were
detected and are marked by arrows in Fig. 3A.
These two protein-DNA complexes were competed by specific subregions of
the promoter. Competition with an Sp1 oligonucleotide eliminated the
slower migrating complex but not the faster migrating protein-DNA
complex. Competition with promoter DNA of decreasing size narrowed down
the region responsible for the formation of the faster mobility complex
to 41 bp spanning the transcription start site (boxed in Fig. 3C). Shorter oligonucleotides covering positions
30-56, 35-65, 45-71, 61-87, and 76-92
(see Fig. 3and Fig. 7) and a TATA-binding protein
oligonucleotide were not able to compete for formation of this complex
(data not shown). A specific protein complex was formed with a 41-bp
labeled probe (PCR #79) corresponding to this region (Fig. 3B). However, the increased amount of nonspecific
binding implies that specificity determinants may have been left out of
this 41-bp promoter fragment. In order to further characterize the DNA
sequence that mediates the formation of the protein-DNA complex close
to the transcription start site, we performed DNase I and methylation
interference assays. The DNA region shown in Fig. 3C was isolated from pSma-2 as a HindIII/XmaI
fragment and used as a probe. A DNase I footprint was not obtained.
Instead, protein binding resulted in a DNase I-hypersensitive site on
the noncoding strand just in front of the AIRC transcription
start site (Fig. 4B). No such effect was observed on
the other strand (data not shown). Methylation interference assays
implicated essential amino acid contacts with several guanine residues
about one turn of the helix upstream of the DNase I-hypersensitive site
relative to the AIRC transcription start (Fig. 4A). Methylation of 5 guanines on the top strand
and 2 on the bottom strand interfered with complex formation.
Figure 4:
Methylation interference and DNase I
assays for the AIRC Inr region. A, methylation
interference assay. The promoter fragment shown in Fig. 3was
methylated. The piperidine cleavage reactions of the free (F),
nonbound (N), and bound (B) DNA are shown.
Interfering methylated nucleotides are noted with an asterisk.
The position of G residues in the top strand around the binding site is
noted with a line. B, DNase I cleavage of the bottom AIRC noncoding strand. Binding of nuclear extract resulted in
the hypersensitive site marked by the arrow.
By
virtue of its position around the AIRC transcription start
site and its capacity to activate transcription at distinct positions
in the absence of a TATA box, we infer that the site described above
may represent an Inr-like element that affects transcription
bidirectionally. This element does not have sequence similarity with
known Inr elements (Azizkhan et al., 1993; Weis and Reinberg,
1992). Interestingly, an overlapping stretch of 13 nucleotides (see Fig. 7) has similarity with the adenovirus major late promoter
Inr (Weis and Reinberg, 1992). However, this element does not appear to
contribute to protein binding in this region, because the competition
experiments showed that most of it is dispensable for binding, and a
30-bp double-stranded oligonucleotide, nucleotides 35-65 (see Fig. 3and Fig. 7), encompassing this region of homology
did not compete either.
Bidirectional Elements between the Transcriptional Start
Sites for GPAT and AIRCThree of the internal deletions
constructed between SmaI site 2 and site 7 resulted in
decreased bidirectional promoter activity. Deletion 2.3 removes two GC
boxes, deletion 3.4 removes two CCAAT boxes and an overlapping GC box,
and deletion 5.6 removes a CCAAT box (see Fig. 1B and Fig. 7). These mutations reduced transcription in both
directions to between 20 and 60% of the intact promoter in both cell
lines. A larger effect was seen for the cognate side, but, overall,
elements in these deletions were required for full expression on both
sides. In each case, the defects were more prominent in HepG2 cells
than in the LMH line. GC and CCAAT boxes between sites 2 and 4 and
between sites 5 and 6 are thus implicated in bidirectional
transcription.HeLa nuclear extracts and a SmaI/AvaI restriction fragment from plasmid pSma-2
(nucleotides 90-188, see Fig. 7) were used to detect
protein-DNA complexes in the 2.4 subsection of the promoter. A specific
complex was detected that was readily competed with an Sp1
oligonucleotide (Fig. 5) but not by a CTF/NF1 oligonucleotide
(Chodosh et al., 1988) (data not shown). This result provides
evidence for the binding of Sp1 to one or more of the three Sp1 sites
in the 2.4 promoter region. No other complexes were detected using this
probe or a probe encompassing sequences downstream of the AvaI
site up to point 7 on the GPAT side under the conditions used.
Thus, specific protein complexes with CCAAT motifs were not detected.
Figure 5:
Sp1 binding in the promoter. The SmaI/AvaI fragment containing 2.4 DNA from plasmid
pSma2 was used as a labeled probe, and an Sp1 oligonucleotide was used
as competitor. The molar excess of the competitor is given above the lanes. The nonspecific competitor is the pBluescript
polylinker used in 100-fold molar excess. The arrow points to
the specific complex.
Deletion 4.5 also had a bidirectional effect, but, in contrast to
the mutations described above, it resulted in increased transcription
on both sides. This could result from removal of a repression element
analogous to a structural control element in the dihydrofolate
reductase (DHFR) promoter (Azizkhan et al., 1993) or
could be because interactions required for bidirectional transcription
are distance-dependent.
Sites Specific for GPAT TranscriptionSequences
within SmaI positions 6-9, flanking the GPAT transcription initiation site, have a predominantly unidirectional
effect on GPAT transcription. Deletion 6.7, which removes a GC
box and disrupts three of six direct repeats (see Fig. 7), had
no significant effect on AIRC transcription strength but
reduced GPAT transcription to 50% or less of the wild type in
LMH and HepG2 cells (Fig. 2). Deletion 7.8 removes the GPAT transcription start site and flanking sequences as well as three
copies of the direct repeats (see Fig. 7). The effects of this
mutation were similar to those of deletion 6.7. Expression from the GPAT side was reduced to less than 50% of the wild type,
whereas AIRC transcription was less affected. The 25-bp region
between SmaI sites 8 and 9 contains an octamer-like motif (see Fig. 1and Fig. 7) that was deleted in combination with
segment 7.8 in the 7.9 mutant. We compared transcriptional activity in
mutants 7.8 and 7.9 to assess the importance of the octamer-like motif
in expression. By this analysis the 7.9 deletion had somewhat different
effects in HepG2 and LMH cells. In both cell lines the major effect was
reduced transcription from the GPAT direction compared with
the intact promoter. In HepG2 cells transcription from the GPAT side was reduced from about 45% of wild type in deletion 7.8 to
less than 15% of wild type in deletion 7.9, consistent with an
essential role for the octamer-like site. However, in LMH cells,
deletion of the 8.9 DNA with the octamer-like motif increased GPAT expression from 21% of wild type in deletion 7.8 to 43% of wild
type in deletion 7.9. The basis for the discordant results is not
presently known.In order to search for protein-DNA interactions in
the promoter region between SmaI sites 6 and 9, gel mobility
shift assays were carried out with two DNA probes. The first probe was
isolated as an AvaI/SmaI fragment from pSma-7 (see Fig. 7, nucleotides 188-262). Specific binding was not
detected in this region (data not shown), even though it appears to
contain the cis-acting sites needed for GPAT transcription (Fig. 2). This may reflect weak interactions
in this region of the promoter that need the presence of distal
sequences for stabilization. The second probe was isolated from plasmid
pSma-7 as an XmaI/SalI fragment (see Fig. 7,
nucleotides 262-349). Two specific complexes were detected using
this probe and HeLa nuclear extract (Fig. 6, A and B). Both were competed with an octamer-containing
oligonucleotide but not by nonspecific DNA. The two bands may result
either from two proteins binding on this site or from protein-protein
interactions resulting in the second complex that migrates more slowly.
A DNase I footprint was obtained between nucleotides 314-334 on
the top strand and nucleotides 320-339 on the bottom strand (Fig. 6C). These positions encompass the octamer-like
motif downstream of the GPAT transcription start site (Fig. 7).
Figure 6:
Protein binding to the GPAT octamer-like motif. A, gel retardation assay and
competition by octamer DNA. The DNA complex was formed with HeLa
nuclear extract and an XmaI/SalI end-labeled probe
from plasmid pSma-7. Arrows point to specific complexes. Molar
excess of an octamer-containing oligonucleotide is shown. B,
effect of nonspecific pBluescript polylinker competitor (100-fold
excess). C, DNase I footprints of the octamer-like site. The
protein-DNA complex was formed with HeLa nuclear extract and an AvaI/SalI probe labeled on either strand. Lanes are
shown for 0(-), 50 µg (+), and 100 µg (++)
of protein. Nucleotide positions were determined by an adjacent dideoxy
sequencing ladder alongside (not shown). The boundaries for the
protected regions are numbered according to the sequence in Fig. 7.
Sites for AIRC TranscriptionDeletion 0.1, which
removes a potential Sp1 site, has a predominantly unidirectional effect
on transcription. The 0.1 promoter mutation showed decreased activity,
about 40% of the wild type, only on the AIRC side in HepG2
cells (Fig. 2). An Sp1 oligonucleotide competed for the
formation of the lower mobility complex detected with a 0.2 DNA probe (Fig. 3A). Thus, the GC box found downstream of the AIRC transcription start site was implicated in mediating
transcriptional activation of the AIRC side of the promoter.
It is not known why formation of the Sp1 complex was decreased in some
experiments (Fig. 3A).
Half-promoters and Internal InversionLarger
deletions and an internal inversion were constructed in order to
determine whether two separate promoters can be derived from this
single bidirectional promoter and to define the contribution of
internal elements to the relative strength of the two sides. Deletion
0.4, which removes all of the AIRC proximal sites, abolished
transcription not only from the AIRC side but also from the GPAT side (Fig. 2). The 5.9 deletion was qualitatively
similar to that of 0.4, but in this case transcription from both
directions was reduced to 20-30% of the wild type. This
reinforces the notion that the most important cis-elements for
bidirectional transcription are to be found on the AIRC side.
Even though the AIRC half-promoter had residual function, its
function was bidirectional. Thus, by this analysis, it was not possible
to dissect the intergenic region into two unidirectional promoters. Construct 2.7i is an inversion of the bidirectional promoter between
points 2 and 7. With this inversion we expected to see increased
transcription from the GPAT direction and a corresponding
decrease from the AIRC side. This would allow an estimate of
the relative contribution of Inr-like element(s) to transcription of
both sides. However, transcription from both directions decreased
relative to the wild type. This would appear to reflect a defined
organization of sites with restricted interplay between elements that
are at and that flank the sites for transcription initiation.
DISCUSSION
Earlier work has established that the chicken GPAT and AIRC genes are tightly linked and divergently
transcribed from an intergenic region of about 230 bp (Gavalas et
al., 1993). Operationally, the intergenic region was referred to
as a bidirectional promoter. The objective of this work was to identify cis-elements that are important for promoter function,
identify potential initiator elements in the TATA-less promoter that
direct transcription initiation from well defined points, and
distinguish between two models for bidirectional transcription: a model
in which bidirectional transcription is driven by two largely
independent promoters arranged back-to-back and a model in which a
bidirectional promoter drives expression of both genes. In the former
case, transcription of each gene should be driven using its own set of cis-acting sites, whereas in the latter case shared cis-elements would be used for transcription from both sides.
In order to address these questions, potential cis-elements
were inferred in the promoter sequence, and the promoter was scanned by
deletion mutagenesis. The function of the mutant promoters was then
tested in a bireporter vector that allowed a simultaneous assay of the
effect of each deletion in both directions. The results support a model
in which several important cis-elements function
bidirectionally, and, therefore, expression of these genes is tightly
coupled using these elements. Fig. 7gives an overview of the
basal promoter sequence and the elements to be discussed. This sequence
includes the intergenic region plus approximately 60 bp encoding the
5`-untranslated region of each mRNA. An important element required
for bidirectional transcription overlaps the AIRC transcription start site. The boundaries of this element within
the 1.2 sequence shown in Fig. 7were mapped by protein-DNA
binding. By virtue of its requirement for transcription and a position
overlapping the site for transcription initiation, we refer to this cis-element as Inr-like. There are at least three classes
of Inr elements in RNA polymerase II-transcribed promoters (Azizkhan et al., 1993; Weis and Reinberg, 1992). A 17-bp element around
the transcription start site of the terminal
deoxynucleotidyltransferase gene (Weis and Reinberg, 1992) directs
transcription from a single nucleotide in vivo and in
vitro and has a CTCANTCT consensus sequence, where the underlined
nucleotide represents the initiation site. Adenovirus major late and
IVa2 promoter Inr elements (Smale and Baltimore, 1989) and the
porphobilinogen deaminase gene Inr (Beaupain et al., 1990)
belong to this class. The minimal promoter elements required for
expression of the dihydrofolate reductase DHFR gene are an Sp1
site and the DHFR Inr, which represents the second class of
Inr elements. This Inr element is required for the hamster, mouse, and
human DHFR genes (Azizkhan et al., 1993) and genes
for hypoxanthine phosphoribosyltransferase, Ki-Ras, 3-phosphoglycerate
kinase, osteonectin, and interferon regulatory factor 1 (Linton et
al., 1989, and references therein). The adeno-associated virus
type 2 p5 promoter has a third class of initiator that can function by
itself or can direct TATA- and Sp1- activated transcription (Seto et al., 1991). A similar element is found in the TATA-less
promoter of the human DNA polymerase gene (Weis and Reinberg,
1992). The AIRC Inr-like element has no sequence similarity
with the types of Inr elements mentioned above. A unique feature of
this element is its bidirectionality. The AIRC Inr-like
element may mediate assembly of the basal transcription machinery on
both sides or do so only for the AIRC side, and it acts as a
transcriptional activator for the distal side of the promoter. The
experiments described here defined this element as a 41-bp region,
which is unusually long compared with other types of Inr elements. Part
of this element is an imperfect palindrome with a 3-bp spacer (Fig. 7). Further experiments will be needed to establish
whether mutations in this region affect the selection of the
transcription start site and whether this element is able to direct
basal transcription in the absence of any upstream activator elements. Apart from the AIRC Inr-like element, other sites were
shown to be important for bidirectional transcription. AIRC proximal GC boxes in region 2.4 are required for transcription of AIRC and GPAT. It is likely but was not directly
established that the two CCAAT boxes in fragment 3.4 contribute to the
function of this region in bidirectional transcription. Direct evidence
for the role of the two CCAAT boxes in fragments 3.4 and the one in
fragment 5.6 would require more precise mutational disruption or
detection of specific protein complexes with these sites. The
bidirectionality of the GC and CCAAT elements in the GPAT/AIRC promoter is not surprising, because they function in both
orientations upstream of the transcription start sites of their target
genes (Wingender, 1990). Examples for activation of bidirectional
transcription include a GC box in the center of the 130-bp intergenic
region for the 1(IV) and 2(IV) collagen genes (Heikkila et al., 1993), a GC box in exon 1 of the 2(IV) gene
(Heikkila et al., 1993), and GC boxes between the
transcription start sites of DHFR and Rep-1 (Fujii et al., 1992). Aside from sequences that activate GPAT-AIRC bidirectional transcription, several cis-elements influence only one promoter side. A GC box
downstream of the AIRC transcription start site enhances
expression of its cognate side. Sequences upstream and around the GPAT transcription start site in regions 6.7 and 7.8,
respectively, function to activate transcription from this side.
Downstream from the GPAT transcription start site an
octamer-like motif, ATGTAAAT (differing by only 1 nucleotide from the
consensus ATGCAAAT), was implicated in full expression of the GPAT side. The octamer motif can mediate activation of transcription by
a subfamily of the POU transcription factors, the octamer-binding
factors (Herr, 1992). Oct-1, the best characterized of its class, is
broadly expressed and regulates transcription of small nuclear RNAs,
histone H2B, and others via the ATGCAAAT motif. Other octamer-binding
factors, such as Oct-2, Oct-4, and Oct-6, are expressed in a temporally
and spatially restricted manner and are involved in developmental
regulation (Schöler, 1991). The positioning of the
element downstream of the GPAT transcription start site is
peculiar to this promoter, because octamer motifs are generally found
upstream of the transcription initiation site of their target gene. Deletion 4.5 in the middle of the promoter resulted in increased
activity on both sides. In the absence of recognizable sequence motifs,
this result may reflect a distance-dependent effect for cooperation of
the two promoter sides or the presence of an uncharacterized
repressor-like structural control element analogous to that of the DHFR/Rep-1 promoter (Azizkhan et al., 1993).
Decreased bidirectional transcriptional activity in mutant 2.7i
emphasizes the importance of correct alignment of activator sequences
and Inr elements for maximal activity. Earlier experiments (Gavalas et al., 1993) suggest that the GPAT and AIRC half-promoters retained 30 and 80% of the wild type activity for
their cognate side, respectively. However, in these mutants, promoter
context was altered with respect to upstream flanking sequences. These
changes altered the vector substantially and made the comparison with
the wild type less reliable than in the present work. Here, the
sequence context was maintained in the half-promoter mutants; the
vector was not altered. Therefore, we consider the results that
indicate that the GPAT half-promoter has essentially no
activity and that the AIRC half-promoter retains approximately
20-40% of the bidirectional activity to be a better approximation
of function. A number of genes in vertebrates are divergently
transcribed from a bidirectional promoter element. These include the
housekeeping genes surf-1 and surf-2 of the surfeit locus (Colombo et al., 1992), the murine and
human 1(IV) and 2(IV) collagen genes (Shimada et
al., 1989; Soininen et al., 1988), histone H2A and H2B
genes (Hentschel and Birnstiel, 1981), the DHFR and Rep-1 genes (Linton et al., 1989; Schilling and Farnham, 1989),
and the Wilms tumor locus (Huang et al., 1990). In other cases
of bidirectional transcription, genes were not identified for both
sides. These include the proliferating cell nuclear antigen gene
promoter (Rizzo et al., 1990), an SV40-like monkey genomic
locus (Saffer and Singer, 1984), the HTF9 CpG island (Lavia et
al., 1987), the human histidyl-tRNA synthase gene (Tsui et
al., 1993), the c-myc oncogene promoter (Chang et
al., 1991), and the VH441 promoter of the heavy chain
immunoglobulin promoter (Nguyen et al., 1991). The AIRC/GPAT locus is the only case where two genes encoding
enzymes of the same pathway are closely linked. This linkage may
provide for co-regulation, but it is not a prerequisite of it, because
five of seven human genes for AMP synthesis are found on different
chromosomes. Given the properties of the AIRC Inr-like
element, a number of models may explain how bidirectional transcription
occurs from this promoter. Two basal transcription complexes
(Buratowski, 1994) may assemble independently on each transcription
start site. In this case, the protein(s) binding on the AIRC Inr would direct assembly of the transcription complex on the AIRC side, and it acts as a transcriptional activator(s) for
the distal GPAT side. Alternatively, transcriptional complexes
having two orientations may assemble on an AIRC Inr. This
would fit with the palindromic nature of the AIRC Inr and the
bidirectional activity of deletion 5.9. Another possibility is that the AIRC and GPAT transcription start sites are close in
space, through looping of the central promoter region, and, therefore,
the AIRC Inr is able to direct assembly of the basal
transcription complexes on both sites. The data currently available do
not distinguish among these possibilities.
FOOTNOTES
- *
- This
research was supported by National Institutes of Health Grant GM46466.
Oligonucleotides were synthesized by the Purdue Laboratory for
Macromolecular Structure supported by National Institutes of Health
Diabetes Research and Training Grant DK20524. This is Journal Paper
14158 from the Purdue University Agricultural Research Station. The
costs of publication of this article were defrayed in part by the
payment of page charges. This article must therefore by hereby marked
``advertisement'' in accordance with 18 U.S.C.
Section 1734 solely to indicate this fact.
The nucleotide
sequence(s) reported in this paper has been submitted to the
GenBank(TM)/EMBL Data Bank with accession number(s)
L12533[GenBank].
- §
- Present address: Laboratoire de
Génétique Moleculaire des
Eukaryotes, Institut de Chimie Biologique, Rue Humann 11, 67085
Strasbourg, France.
- ¶
- To whom correspondence
should be addressed: Dept. of Biochemistry, Purdue University, 1153
Biochemistry Bldg., West Lafayette, IN 47907. Tel.: 317-494-1618; Fax:
317-494-7897; Zalkin{at}biochem.purdue.edu.
- (
) - The abbreviations used are: bp, base pair(s);
Inr, initiator; CAT, chloramphenicol acetyltransferase; LUC,
luciferase; PCR, polymerase chain reaction.
ACKNOWLEDGEMENTS
We thank P. Stockbine and David Williams (State
University of New York at Stony Brook) for the generous gift of LMH
cells and P. Guo and E. Scholz (Purdue University) for help with the
cell cultures and transfections.
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©1995 by The American Society for Biochemistry and Molecular Biology, Inc.

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