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Molecular and Cellular Biology, June 1999, p. 4270-4278, Vol. 19, No. 6
0270-7306/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.
Cell Cycle Regulation of DNA Replication Initiator
Factor Dbf4p
Liang
Cheng,
Tim
Collyer, and
Christopher F. J.
Hardy*
Department of Cell Biology and Physiology and
Department of Genetics, Washington University School of Medicine,
St. Louis, Missouri 63110
Received 9 October 1998/Returned for modification 25 November
1998/Accepted 9 March 1999
 |
ABSTRACT |
The precise duplication of eukaryotic genetic material takes place
once and only once per cell cycle and is dependent on the completion of
the previous mitosis. Two evolutionarily conserved kinases, the cyclin
B (Clb)/cyclin-dependent kinase (Cdk/Cdc28p) and Cdc7p along with its
interacting factor Dbf4p, are required late in G1 to
initiate DNA replication. We have determined that the levels of Dbf4p
are cell cycle regulated. Dbf4p levels increase as cells begin S phase
and remain high through late mitosis, after which they decline
dramatically as cells begin the next cell cycle. We report that Dbf4p
levels are sensitive to mutations in key components of the
anaphase-promoting complex (APC). In addition, Dbf4p is modified in
response to DNA damage, and this modification is dependent upon the DNA
damage response pathway. We had previously shown that Dbf4p interacts
with the M phase polo-like kinase Cdc5p, a key regulator of the APC
late in mitosis. These results further link the actions of the
initiator protein, Dbf4p, to the completion of mitosis and suggest
possible roles for Dbf4p during progression through mitosis.
 |
INTRODUCTION |
Eukaryotic DNA replication is
initiated during the synthesis (S) phase of the mitotic cell cycle at
multiple chromosomal sites designated origins. Segregation of newly
replicated chromosomes occurs during mitosis (M phase) and is separated
from S phase by two gaps, G1 and G2. The
multiple origins on a chromosome initiate replication at various times
from early to late in S phase (16, 17, 19). Initiation from
individual origins happens at most once per S phase, and reinitiation
is prevented until the cell has finished M phase (36). The
mechanism by which the cell regulates the timing of initiation of DNA
replication and prevents reinitiation until the completion of mitosis
has not been defined.
In budding yeast there are at least two complexes present at origins
(13). A postreplication complex, which consists of at least
the origin recognition complex, is detected after initiation during S
phase and is present until late in M (13). This complex is
modified late in M, giving rise to the prereplication complex. The
prereplication complex is present from late M to S phase and is most
probably formed through the association of Cdc6p and the MCM family of
six proteins with origins (3, 8, 40). Cdc6p becomes
associated with chromatin and origins late in M and dissociates late in
G1 or early in S (40). The MCM proteins
associate with origin sequences late in mitosis or early in
G1, and their release from origins is coincident with
replication initiation (3, 40). Precisely how the cell cycle
machinery is linked to replication through regulation of the
transitions between these two complexes late in M and again late in
G1 is not known.
Two evolutionarily conserved kinases, the cyclin B
(Clb)/cyclin-dependent kinase (Cdk/Cdc28p) (13) and Cdc7p
along with its interacting factor Dbf4p, are required late in
G1 to initiate DNA replication (5, 22, 25, 31).
Cdc7p kinase activity peaks late in the G1 phase of the
cell cycle (25), and Cdc7p is required for origin firing
during S phase (4, 10). Based on a series of one-hybrid
studies, Dbf4p is thought to be targeted to origins (12,
21). We reported the identification in Saccharomyces cerevisiae of a recessive loss-of-function mutation in
MCM5/CDC46, cdc46-bob1, which bypasses the
requirement for Dbf4p-Cdc7p (20). A recent report from
Tanaka et al. shows that dbf4-1 cells fail to release MCM
proteins from origins under restrictive growth conditions
(40). These results suggest a role for Dbf4p-Cdc7p as a
modifier of MCM function at origins, late in G1 or early in
S. Consistent with this model, Mcm2p is a target of Dbf4p-Cdc7p during
initiation of DNA replication (32).
Our previous studies indicate that Cdc5p interacts with Dbf4p
(21). Cdc5p is a member of the polo-like kinase family. It accumulates in the nuclei of M cells (7, 35) and is thought to play roles both in anaphase-promoting complex (APC) regulation late
in M (6, 35) and in adaptation to the DNA damage checkpoint in metaphase-arrested cells (41). The interaction with Cdc5p suggested that Dbf4p might have an M phase function in addition to its
S phase roles (21). In this study we have further developed links between Dbf4p and mitosis. Specifically, we show that the levels
of Dbf4p fluctuate during the cell cycle and that Dbf4p accumulates in
the nuclei of late G1, S, and M phase cells. The levels of
Dbf4p decline dramatically as cells exit mitosis, and they are
sensitive to mutations in key APC components. In addition, we show that
Dbf4p is modified in cdc13-1 cells grown at the restrictive temperature and that this modification is dependent on key components of the DNA damage checkpoint pathway. We speculate that Dbf4p may
provide a link between mitosis and S phase through its interactions with the M and S phase regulators, Cdc5p and Cdc7p, respectively.
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MATERIALS AND METHODS |
Plasmids and strains.
Yeast strains used in this study are
listed in Table 1. Plasmid DNA was
transformed into yeast by the lithium acetate method as described
previously (24). Yeast strains without plasmids were grown
in yeast extract-peptone-dextrose. YEP medium contained 1% yeast
extract and 2% Bacto Peptone. Yeast strains bearing plasmids were
grown in selective synthetic medium (SC) with 2% sugar (galactose or
raffinose as indicated). Strains with plasmids to be induced with
galactose were first grown in synthetic medium with 2% raffinose to an
A600 of 0.2 to 0.4. Wild-type strains were grown
at 30°C unless noted otherwise. pCH920 carries the DBF4
open reading frame ligated into the BamHI-XhoI
site of pCH765 (pRS423-GAL1-HA). The GAL-HA-dbf4
70 plasmid (pCH955) was created by deleting
DBF4 sequences from position +1 to +210 by PCR.
ProA tagging of Dbf4p.
The chromosomal copy of the
DBF4 gene was tagged by a C-terminal, in-frame integration
of a DNA fragment encoding the immunoglobulin G (IgG) binding domains
of protein A (42). The protein A (ProA) gene and adjacent
HIS3 and URA3 markers were amplified by PCR with
pProA-HIS3-URA3 (a gift from Mike Rout and John Aitchison) (1). The following primers were used for the PCR:
DBF4 sense primer, 5'-GAA AAC GAT TTA AAT TTT GAG GCT ATT
GAC TCG TTA ATT GAA AAT CTC AGA TTT CAA ATA GGT GAA GCT CAA AAA CTT
AAT-3'; DBF4 antisense primer, 5'-CAA TAA CAT TGC CGT TGA
TAG CTT TTT TGT TCC GAG CAG CAA TGG AAA CGG AAC AAT ACT TTT ACT TAT AAT
ACA GTT TTT TAG-3'. The 5' region of the sense primer encodes the
carboxy-terminal 20 amino acids of Dbf4p (up to but not including the
stop codon) and continues in frame to encode the 7 amino acids of ProA
beginning with the glycine at amino acid residue 24 (42).
The 5' region of the antisense primer corresponds to nucleotides 2220 to 2161 of the untranslated region of DBF4 (1 is the A of
the initiation codon) and continues with 24 nucleotides, 1050 to 1027, of the reverse complement of the URA3 gene. The PCR products
were transformed into yeast, and HIS+ URA+
transformants were screened by Western analysis for expression of
Dbf4-ProA.
Immunofluorescence.
Indirect immunofluorescence was carried
out exactly as described previously (45). For localization
of the epitope-tagged Dbf4p (Dbf4-ProA), wild-type strains were grown
to early log phase and prepared for immunofluorescence microscopy.
Cells from the various temperature-sensitive strains used in this study
were grown to early log phase at 24°C and then transferred to 37°C for 3 to 4 h, at which time greater than 90% of the population exhibited the arrest morphology.
-factor and nocodazole arrests were
conducted with cells in early log phase as described previously (18) and as described by Jacobs et al. (26),
respectively. The DNA content of these samples was determined by
fluorescence-activated cell sorter (FACS) analysis (see Fig. 2d). When
Dbf4-ProA was visualized, cells were fixed for 10 min. The fixed cells
were incubated first with affinity-purified rabbit anti-mouse IgG
(Cappel catalog no. 55480) and then with donkey anti-rabbit IgG
(Chemicon catalog no. AP182F) fluorescein-conjugated secondary
antibody. Photographs were taken with a 100× objective on a Olympus
microscope with Kodak T-MAX400 film processed at 400 ASA.
Immunoprecipitation.
Cells were pelleted, washed once in
water, and lysed or frozen in liquid nitrogen. Pellets were resuspended
in 0.3 ml of lysis buffer containing 5% glycerol, 20 mM Tris-HCl (pH
8.0), 1 mM EDTA, 10 mM MgCl2, 0.3 M AmSO4, 1 mM
dithiothreitol, 1 mM benzamidine, 1 mM phenylmethylsulfonyl fluoride, 5 mg of leupeptin per ml, 2 mM pepstatin A, 50 mM NaF, 10 mM sodium
pyrophosphate, and 0.5 mM Na-VO4. The cells were lysed by
adding 0.5 ml of acid-washed glass beads and vortexing in pulses until
90% lysis was achieved, and then 0.35 ml of immunoprecipitation buffer
(1 M LiCl, 2% Triton X-100, 10% glycerol, 0.5 mM Na-VO4,
and protease inhibitors as described for lysis buffer) was added and
vortexed for 1 min. The lysate was spun for 10 min at 3,000 rpm
(Heraeus-Picofuge) and the supernatant was aliquoted and frozen in
liquid nitrogen. Protein concentrations were determined with the
Bio-Rad protein assay. Four hundred milligrams of lysate was incubated
with 0.1 ml of IgG-Sepharose (Pharmacia) at 4°C for 1.5 h.
Immunoprecipitates were pelleted by centrifugation, washed two times
with immunoprecipitation buffer and then two times with CIP buffer (50 mM HEPES, 10 mM MgCl2, and 5 mM MnCl2), and
divided into two samples. One hundred units of calf intestinal
phosphatase (CIP) was added to one of the samples but not to the other.
To this suspension an equal volume of sodium dodecyl sulfate (SDS)
gel-loading buffer was added, and the mixture was incubated for 5 min
at 100°C and subjected to electrophoresis on an SDS-7%
polyacrylamide gel. Proteins were electrophoretically transferred to
nitrocellulose membranes. Blots were incubated with primary antibody
(rabbit anti-mouse IgG [Cappel catalog no. 55480]) for 1 h at
room temperature in 10 mM Tris-Cl (pH 7.5)-150 mM NaCl-0.05% Tween
20 (TBST) with 2% nonfat milk. The immunoblots were washed with TBST
and then incubated for 1 h with secondary antibody (alkaline
phosphatase-conjugated anti-rabbit IgG) in TBST. The immunoblots were
washed again in TBST and developed via color visualization with
nitroblue tetrazolium and 5-bromo-4-chloro-3-indolyl-1-phosphate (Promega).
Other methods.
Hydroxyurea was obtained from Sigma and used
at a final concentration of 200 mM.
-factor was obtained from Sigma
and for bar1 mutant and wild-type cells was used at final
concentrations of 0.2 µM and 5 mg/ml, respectively. Nocodazole was
obtained from Aldrich and was added to medium from a 20-mg/ml stock
solution in dimethyl sulfoxide. It was used at a final concentration of 20 µg of nocadazole per ml and 1% dimethyl sulfoxide, as described by Jacobs et al. (26). The DNA content of cells was measured on a Becton Dickinson (San Jose, Calif.) FACSsan as described by
Epstein and Cross (15).
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RESULTS |
Dbf4p is cell cycle regulated.
The DBF4 message is
constitutively present during the cell cycle, peaking in
G1/S (5). To determine the pattern of Dbf4p localization and its regulation during the cell cycle, the chromosomal copy of DBF4 was replaced with sequence encoding an ProA
epitope-tagged version (the five IgG binding domains of ProA fused in
frame at the C terminus) (42). The Dbf4-ProA-tagged strain
exhibited no growth defects, and therefore the Dbf4-ProA fusion
performed all the essential functions of Dbf4p. We initially examined
the fluctuations of Dbf4p levels in a population of G1
cells synchronously released from an
-factor-induced G1
arrest state. Progression through a single cell cycle was monitored by
FACS analysis to determine DNA content and by budding index (Fig.
1c). Immunoblot analysis was also
performed with extracts derived from these synchronized cells, and
Dbf4-ProA was detected as a 120-kDa band. As shown in Fig. 1a,
Dbf4-ProA was not detected in extracts derived from cells arrested in
G1 with
-factor. Dbf4-ProA began to accumulate as cells
were released from the block, completed G1, and entered S
phase. Dbf4p levels remained high as cells progressed through mitosis
and declined dramatically as the cells completed mitosis and entered
G1 of the next cell cycle.

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FIG. 1.
Dbf4p levels fluctuate during the cell cycle.
DBF4-proA (YCH288) cells were synchronized in G1
by addition of -factor and released into fresh medium lacking
-factor at 25°C. Samples for FACS analysis and extract preparation
were taken at the times shown. (a and b) Dbf4-ProA (a) and actin (b)
were detected by immunoblotting with anti-IgG and antiactin antibodies,
respectively. (c) FACS analysis of DNA content. The percentage of
unbudded cells is shown on the right of the FACS analysis profile.
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Dbf4p accumulates in the nuclei of G1-, S-, and
M-phase-arrested cells.
To more fully determine the subcellular
pattern of Dbf4p localization and accumulation during the cell cycle,
DBF4-proA was expressed in a panel of cdc mutant
strains, and immunoblot and immunofluorescence analyses were performed
with the temperature-arrested cells. The arrest state of these cells
was determined by FACS analysis (Fig.
2d). As shown in Fig. 1a and 2a,
Dbf4-ProA was not detected in extracts derived from cells arrested in
late G1 with
-factor. However, Dbf4-ProA was detected in
cdc4-1 late-G1-arrested cells (Fig. 2a).
Dbf4-ProA was also detected by immunoblot analysis in extracts derived
from cells synchronized in S phase (with hydroxyurea), in metaphase
(cdc13-1 cells grown at the restrictive temperature and
cells treated with nocadazole), and late in M (cdc14-1 and cdc5-1 cells grown at the restrictive temperature) (Fig.
2a). The levels of Dbf4-ProA in arrested cdc23-1 cells were
significantly lower than the levels of Dbf4p in nocadazole-arrested
cells. As Cdc23p is a component of the APC, we analyzed the Dbf4p
levels in two other mutant strains that are defective for other
components of the APC. We examined Dbf4p levels in cdc16-1
(Fig. 2a) and cdc27-2 (data not shown) cells grown at the
permissive and restrictive temperatures. By immunoblotting, the levels
of Dbf4p in arrested cdc16-1 and cdc27-2 cells
were comparable to, if not higher than, the level of Dbf4p present in
nocadazole-arrested cells.

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FIG. 2.
Dbf4p is present in late G1 to late M phase
synchronized cells. Wild-type and cdc mutant cells
expressing an integrated ProA tagged copy of Dbf4p were grown
asynchronously or arrested in different stages of the cell cycle either
by using chemicals or by growth of the cdc mutant at the
restrictive temperature. Late G1, -factor (YCH201) and
cdc4-1 (YCH215); S, hydroxyurea (HU) (YCH201); metaphase,
cdc13-1 (YCH216), nocodazole (NZ) (YCH201), and
cdc23-1 (YCH217); telophase, cdc14-1 (YCH219) and
cdc5-1 (YCH218). Extracts were derived from these cells, and
the levels of Dbf4-ProA (a) and actin (b) were determined by
immunoblotting with anti-IgG and antiactin antibodies, respectively.
(c) Immunoblot analysis of Dbf4-ProA in cdc16-1 (YCH406)
cells at permissive (23°C) and restrictive (37°C) temperatures. (d)
FACS analysis of the DNA content at the different arrest points.
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Indirect immunofluorescence showed that Dbf4p-ProA was localized
predominantly in the nucleus, and an asynchronous cell population
was
detected in only a subset of the cells (Fig.
3, top panels).
The signal was strongest
in budded cells containing a single nucleus
(possible S,
G
2, and early M phase cells) and was never observed
in
either single cells (G
1 cells) or large budded cells
containing
two nuclei (cells in late mitosis or undergoing cytokinesis)
(Fig.
3 and data not shown). The background signal in the untagged
parental
strain (W303) is shown in Fig.
3, bottom panels.

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FIG. 3.
Detection of Dbf4p by immunofluorescence in mitotic
cells. Cells derived from asynchronous cultures were fixed with
methanol-formaldehyde and processed for indirect immunofluorescence.
(Top) Left panel, population of asynchronous Dbf4-ProA cells (YCH201)
stained with anti-IgG to detect Dbf4-ProA. FITC, fluorescein
isothiocyanate. Right panel, DAPI (4',6-diamidino-2-phenylindole)
staining to detect DNA. An arrow points to a large budded single cell
with a single nucleus. (Bottom) Left panel, population of asynchronous
Dbf4p (untagged) cells (W303-1A) stained with anti-IgG. Right panel,
DAPI staining to detect DNA. All images were taken with a 100×
objective and printed at the same magnification.
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Indirect immunofluorescence analysis was also performed with
synchronized cells. Dbf4-ProA was observed only in the nucleus,
and it
was not present in cells synchronized in G
1 with

-factor.
It was, however, detected in
cdc4-1 cells grown
at the restrictive
temperature, as shown in Fig.
4. A Dbf4-ProA signal was also present
in
cells synchronized in S phase (cells arrested with hydroxyurea)
and in
cells synchronized early in M, during metaphase (
cdc13-1,
nocodazole-treated, and
cdc23-1) cells (Fig.
4). The
localization
results were in general agreement with the immunoblot
analysis,
with the exception of the
cdc23-1 cells (YCH217).
Whereas the
immunoblotting detected a low level of Dbf4-ProA in
arrested
cdc23-1 cells, a strong Dbf4-ProA signal was
detected by immunofluorescence
in the arrested
cdc23-1
cells. The reason for this lack of correlation
is being further
investigated. We speculate that the immunofluorescence
strategy may be
more sensitive and have a lower threshold for
detection of Dbf4p than
the immunoblot.

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FIG. 4.
Dbf4p is present in the nuclei of late G1-
to metaphase-arrested cells. Wild-type and cdc mutant cells
expressing an integrated ProA-tagged copy of Dbf4p were arrested in
different stages of the cell cycle either by using chemicals or by
growth of the cdc mutant at the restrictive temperature.
Immunofluorescence was performed on these cells as described in
Materials and Methods. Two views of each field are shown, Dbf4-ProA
staining (fluorescein isothiocyanate [FITC]) and staining of DNA
(DAPI). All photographs were taken with a 100× objective and printed
at the same magnification. cdc4-1 mutants form abnormal buds
(44). The same cultures were used for immunoblot analysis
(Fig. 2). HU, hydroxyurea; NZ, nocodazole.
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APC mediation of Dbf4p degradation in G1.
Progression through and completion of M requires the
ubiquitin-dependent proteolysis of specific substrates (29).
For example, the metaphase-to-anaphase transition requires degradation
of Pds1p in S. cerevisiae and of cut2 in
Schizosaccharomyces pombe (9, 18). Completion of
M is dependent on the degradation of mitotic cyclins (23, 29, 37,
39, 43). Stage-specific degradation of these cyclins is dependent
on a 20S particle designated the APC or cyclosome, a ubiquitin protein
ligase (30, 38). In addition, the Dbf4p-interacting kinase
Cdc5p is a substrate for the APC late in M (6, 21, 35). The
cell cycle-regulated pattern of Dbf4p protein levels suggested that the
APC/cyclosome might also target Dbf4p for degradation. If APC function
is required for the degradation of Dbf4p, we predicted that the
stability of Dbf4p would be enhanced in cells compromised for APC
function compared to wild-type cells.
To examine whether the APC is involved, the stability of Dbf4p in cells
arrested in G
1, a phase of the cell cycle in which
the APC
is active in Pds1p, Clb2p, and Ase1p degradation (
2,
9,
28,
46), was examined.
CDC23 and
cdc23-1 cells
containing
plasmids expressing hemagglutinin (HA)-Dbf4p under control
of
the
GAL1 promoter were grown in glucose at 23°C,
arrested in G
1 with

-factor, and then shifted to 37°C
to inactivate the
cdc23-1 gene product (
7,
9). At
this point HA-Dbf4p expression was
induced by the addition of
galactose, followed after 30 min by
the addition of glucose to turn off
its expression. The restrictive
temperature (37°C) was maintained
while these steps were performed.
As shown in the immunoblot, HA-Dbf4p
was not detected after 80
min in the wild-type cells (Fig.
5, top). In contrast, the majority
of
HA-Dbf4p was still present after 2 h in the
cdc23-1
cells (Fig.
5, bottom). These results provide evidence that Dbf4p
proteolysis
is APC mediated. It is interesting to note the possible
distinction
between the immunoblot levels of Dbf4p in arrested
cdc23-1 versus
cdc16-1 cells in Fig.
2 (cells
which were not

-factor arrested
before the temperature shift). This
may suggest that for APC-mediated
degradation of Dbf4p outside
G
1, the function of Cdc16p may be
more important than that
of Cdc23p.

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FIG. 5.
Degradation of Dbf4p is dependent on Cdc23p function.
Wild-type (YCH192) and cdc23-1 (YCH208) cells were
transformed with a 2µm-based plasmid carrying GAL1-HA-DBF4
(pCH920). For both strains an overnight culture was grown selectively
at 23°C in SC lacking histidine. This culture was inoculated into YEP
plus raffinose, grown to early log phase at 23°C, and arrested in
G1 with -factor. When >90% of the cells, as determined
by microscopy, exhibited the arrest state, the temperature of the
culture was shifted to 37°C, the restrictive temperature for
cdc23-1 cells. FACS analysis of these blocked samples
indicated that >90% of the cells had a 1N content of DNA and were in
G1 (data not shown). After 30 min at the restrictive
temperature, galactose was added at time 30 to induce expression of
HA-DBF4 from the GAL promoter. Thirty minutes
later, at time zero, glucose was added to turn off expression of
HA-DBF4 from the GAL promoter while maintaining
the G1 arrest at the restrictive temperature. FACS analysis
of these blocked samples also indicated that >90% of the cells had a
1N content of DNA and were in G1 (data not shown). Samples
of equal density were taken at the indicated time points and assayed by
immunoblotting for HA-Dbf4p and actin. Actin detection was used as an
internal loading control.
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The results in Fig.
5 suggested that Dbf4p may have a half-life of as
long as 1 h. Alternatively, the persistence of Dbf4p
in the
cdc23-1 cells seen in Fig.
5 could have been due to a long
half-life for the
DBF4 RNA message. To distinguish between
these
possibilities, we repeated the experiment with the following
modification:
following a 15-min galactose induction of HA-Dbf4p,
glucose (2%)
and cycloheximide (10 µg/ml) were added to repress
transcription
and translation, respectively (Fig.
6B). The majority of the Dbf4p
disappeared within 10 min of the addition of glucose and cycloheximide.
In contrast, under the same conditions, we determined that the
stability of Dbf4p in

-factor-arrested cells was greatly enhanced
in
arrested
cdc16-1 mutant cells (Fig.
6D). This indicates a
Dbf4p
half-life of approximately 5 min and further suggests that Dbf4p
degradation is APC dependent. Such a short half-life for Dbf4p
correlates well with the measured stabilities of other known APC
substrates, including Ase1p and Cdc5p, which also have 5-min half
lives
(
2,
6,
9,
28,
46).

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FIG. 6.
Degradation of Dbf4p depends on sequences containing
destruction boxes. (A) Localization of putative destruction boxes in
Dbf4p and alignment with destruction boxes of other APC substrates. (B
and C) Degradation of Dbf4p in G1 depends on the N-terminal
70 amino acids. Wild-type (WT) cells expressing either HA-tagged Dbf4p
(GAL-HA-DBF4, pCH920) or a version lacking the N-terminal 70 amino acids (GAL-HA-dbf4 N70, pCH955) under the control of
the GAL promoter were arrested in G1 with
-factor. The Dbf4p proteins were detected after induction and
subsequent repression of the GAL promoter as described for
Fig. 5 with the following modification: following a 15-min galactose
induction of HA-Dbf4p, glucose (2%) and cycloheximide (10 µg/ml)
were added to repress transcription and translation, respectively. (D)
Degradation of Dbf4p in G1 depends on the APC gene
component, CDC16. cdc16-1 cells (YCH404) expressing
HA-tagged Dbf4p (GAL-HA-DBF4, pCH920) were arrested in
G1 with -factor and then shifted to 37°C for 15 min
prior to induction. Dbf4p was detected after induction and subsequent
transcriptional and translational repression as described for panels B
and C.
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All known substrates of the APC contain a destruction box motif
characterized by conserved arginine and leucine residues in
positions 1 and 4 of a 9- to 10-amino-acid sequence. This destruction
box is
required for APC-mediated proteolysis and was first identified
in
vertebrate Clb cyclins (
29). The N-terminal region of Dbf4p
contains two putative destruction boxes (Fig.
6A). To test their
role
in Dbf4p degradation, the region containing these motifs
was deleted,
resulting in a deletion of the N-terminal 70 amino
acid residues of
Dbf4p (
dbf4
N70). When expressed in wild-type
cells as for
Fig.
5, the Dbf4

N70 protein was greatly stabilized
compared to Dbf4p
(Fig.
6C). Thus, the region harboring the destruction
box motifs is
necessary for degradation of Dbf4p. These results
provide further
support for the proposal that Dbf4p degradation
is dependent on the
APC.
Modification of Dbf4p in cdc13-1 cells is dependent on
Mec1p.
During the immunoblot analysis of Dbf4p levels in cell
cycle-arrested cells (Fig. 2), we observed that the electrophoretic mobility of Dbf4p was modified in cdc13-1 cells. The
migration of Dbf4p in arrested cdc13-1 cells was notably
slow. In contrast, the shifted form of Dbf4p was not observed in
cycling cells (Fig. 1) or in cells grown in either hydroxyurea or
nocodazole, which arrest in S phase and metaphase, respectively (Fig.
2). The appearance of the modified form of Dbf4p in cdc13-1
cells was further monitored in a time course following a shift of the
cdc13-1 culture to the restrictive temperature (Fig.
7a). We determined that the modified form
of Dbf4p was sensitive to phosphatase treatment (Fig. 7b), and
therefore the shift in arrested cdc13-1 cells was due to
phosphorylation of Dbf4p.

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FIG. 7.
Dbf4p is modified in cdc13-1 cells in a
MEC1-dependent manner. (a) DBF4-proA cdc13-1
(YCH216) cells were incubated at 37°C, the nonpermissive temperature,
for 4 h. Samples for extract preparation were taken at 1-h
intervals. (b) DBF4-proA cdc13-1 (YCH216) cells were grown
at 37°C for 4 h. Dbf4-ProA was immunoprecipitated from extract
by using IgG-Sepharose, washed into CIP buffer, and divided into two
samples. One hundred units of CIP was added to one of the samples (+)
but not to the other ( ). Dbf4-ProA was also immunoprecipitated from
extracts derived from DBF4-proA cdc13-1 (YCH216) cells grown
at the permissive temperature. This sample was not exposed to CIP
( *). All three tubes were placed at 37°C for 30 min. The samples
were loaded onto an SDS-7% polyacrylamide gel, and immunoblot
analysis was performed with anti-IgG to detect Dbf4-ProA. (c)
DBF4-proA cdc13-1 mec1-1 (YCH317) cells were incubated at
37°C for 6 h. Samples for extract preparation were taken at
1-h-intervals. (d) DBF4-proA CDC13 MEC1 (YCH201) cells were
incubated at 37°C. DBF4-proA cdc13-1 MEC1 (YCH216) and
DBF4-proA cdc13-1 mec1-1 (YCH324) cells were incubated at
37°C for 4 and 6 h, respectively. Samples for extract
preparation were taken at these times. Dbf4-ProA and actin were
detected by immunoblotting with anti-IgG and antiactin antibodies,
respectively.
|
|
The
cdc13-1 mutant cells are known to activate the DNA
damage checkpoint when they are grown under restrictive conditions
(
14). Therefore, we next asked whether the
MEC1
gene was necessary
for the modification. The
MEC1 gene
product is required for the
DNA damage checkpoint pathway
(
14). We monitored the shift of
Dbf4p in the
cdc13-1
mec1-1 checkpoint-defective strain by immunoblotting
following
6 h of growth at the restrictive temperature (Fig.
7b).
In this
strain, the shifted form of Dbf4p was not observed (Fig.
7c and d). The
shift was also not observed in the
cdc13-1 rad53-21 checkpoint-defective strain (data not shown). Thus, accumulation
of the
shifted phosphorylated form of Dbf4p is dependent upon
Mec1p and Rad53p
function.
 |
DISCUSSION |
Here we report that the levels of the initiator factor Dbf4p are
cell cycle regulated and decline as cells complete mitosis. Based on
immunoblot and immunofluorescence analyses, Dbf4p accumulates in the
nuclei of late G1, S, and M phase cells, and its levels decline as cells complete M and begin the next cell cycle. It is well
established that progression through and completion of M requires the
ubiquitin-dependent proteolysis of specific substrates (29).
Stage-specific degradation of these factors is dependent on a 20S
particle designated the APC or cyclosome, a ubiquitin protein ligase
(30, 38). We show that the level of Dbf4p is sensitive to
mutations in genes for key APC components, CDC16 and
CDC23, in a manner similar to that for other APC substrates, including Pds1p, Ase1p, Clb cyclins, and the polo-like kinase Cdc5p
(6, 7, 9, 28, 35, 46). The pattern of Dbf4p disappearance
from cells that are completing mitosis and the sensitivity of Dbf4p
degradation during G1 to mutations in components of the APC
suggest that Dbf4p is also targeted for degradation by the APC. In
addition, the destruction of Dbf4p is dependent on prototypic APC
destruction box sequences present in its N-terminal region. We also
show that Dbf4p is modified in arrested cdc13-1 cells which
activate the DNA damage response pathway and that this modification requires the key DNA damage checkpoint genes MEC1 and
RAD53 (14).
Previous studies of Dbf4p function have characterized its interaction
with Cdc7p (12, 21, 25). The Cdc7p protein kinase is
required for firing of origins during S phase (4, 10). Cdc7p
kinase activity peaks during late G1 and is positively
regulated by Dbf4p (25). Moreover, Dbf4p is thought to be
targeted to origins, based on a one-hybrid assay (12, 21).
These results have led to a proposal that the Cdc7p-Dbf4p complex is
recruited to origin complexes where it modifies the prereplication
complex, leading to initiation (12, 13, 21). These results
are consistent with an S phase role for Dbf4p. The results from this
paper, combined with our earlier report documenting a Dbf4p interaction
with the M phase kinase Cdc5p (21), suggest that Dbf4p may
play roles outside S phase.
Dbf4p may mark origins that have initiated DNA replication.
As
discussed above, Dbf4p is required just prior to initiation and likely
interacts with the prereplication complex (27). The
formation of the prereplication complex late in M requires the
recruitment of Cdc6p and MCM proteins (13). Interestingly, Dbf4p function can be bypassed by mcm5-bob1, which contains
a point mutation in MCM5 (20). In addition, Mcm2p
is a target of regulation by Dbf4-Cdc7p during initiation of
replication (32). These results suggest that Dbf4p and MCM
functions are linked. Dbf4p could play a role in the recruitment of MCM
proteins to origins and/or in their removal from origins coincident
with initiation of replication. We propose that the degradation of
Dbf4p late in M may also be part of the process which mediates origin
remodeling late in M. In other words, the destruction of Dbf4p late in
M phase and its coincident removal from postreplication complexes may
facilitate the recruitment of MCM proteins to origins. If this model is
correct, then Dbf4p would be present at origins from just prior to
initiation until late in M, when origins transition from the post- to
the preinitiation complex. It is clear from the evidence in this report
that Dbf4p is present during this interval of the cell cycle (from just
prior to initiation to late in M). If Dbf4p is associated with origins
during this entire interval, it could act as a marker for origins that
have undergone replication during the same cell cycle.
Is Dbf4p a regulator of Cdc5p kinase activity during M?
Dbf4p
interacts with Cdc5p, a member of the polo-like kinase family
(21). The kinase activity of Cdc5p is cell cycle regulated and peaks during M phase (6, 7). Cdc5p plays a key role in
the regulation of the APC late in M (6, 35). Therefore, Dbf4p's main role during mitosis might be as a regulator of Cdc5p kinase activity. What support is there from this work that Cdc5p and
Dbf4p act in concert during mitosis? First, we have determined that
Dbf4p is modified in arrested cdc13-1 cells in a
MEC1- and RAD53-dependent manner. Cdc5p is also
required for adaptation to the DNA damage response. Wild-type yeast
cells exposed to DNA damage activate the DNA damage checkpoint,
resulting in a cell cycle arrest (14). These cells
eventually reenter the cell cycle after an extended metaphase arrest
through a process designated adaptation (41). Restrictive
growth of cdc13-1 CDC5 cells activates the DNA damage
checkpoint and arrests these cells for an extended period in metaphase.
In contrast, cdc13-1 cdc5-ad cells remain arrested in
G2/M following growth at the restrictive temperature (41). Cdc5p, like Dbf4p, is modified in arrested
cdc13-1 cells in a MEC1- and
RAD53-dependent manner (7). It will be
interesting to determine if Dbf4p plays any role in checkpoint
adaptation and if so whether the checkpoint-dependent modifications of
Dbf4p and/or Cdc5p are related to any roles they might play in this adaptation.
Second, strikingly, Dbf4p is targeted for destruction late in M by the
APC, in a manner similar to that for Cdc5p. The other
known substrates
of the APC play key roles during mitosis, and
their removal late in the
cell cycle allows the cell to reset
the cell cycle stage
(
29). A number of APC substrates, including
Cdc5p, Cdc20p,
and Clb/Cdk, also play key roles in regulating
APC function (
6,
29,
35,
44). Taken together, these results
hint at a role for
Dbf4p in regulating APC activity late in M,
perhaps through its
interactions with Cdc5p. However, other results
suggest that Dbf4p does
not play a role in APC regulation. Overexpression
of Clb2p in mutant
cells with APC defects is lethal (
6), whereas
overexpression
of Clb2p does not adversely affect the growth of
a
dbf4-1
mutant (data not shown). In addition, the APC activity
level in
dbf4-1 cells grown at the permissive temperature is
identical
to that in wild-type cells (
6a). Finally,
overexpression of
APC regulators
CDC5 and
HCT1 in
yeast increases APC activity,
leading to a decrease in Clb2p levels
(
6,
44). In contrast,
overexpression of
DBF4 has
no affect on APC activity or Clb2 levels
in cells (
6a).
These results suggest that Dbf4p's interactions
with Cdc5p are not
involved in regulating the
APC.
In conclusion, the cell cycle regulation of Dbf4p and its interactions
with the G
1/S and M phase kinases Cdc7p and Cdc5p,
respectively, suggest that Dbf4p is a link between the factors
which
control M and those which control initiation of DNA replication.
In
order to clarify these interactions, our future studies will
be
directed at understanding both the dynamics of Dbf4p at origins
and the
role of Dbf4p-Cdc5p during
mitosis.
 |
ACKNOWLEDGMENTS |
We thank L. Hartwell, K. Nasmyth, J. Cooper, and M. Rout for
strains and plasmids, and we thank S. Wente for comments on the manuscript.
This work was supported by grant GM5678801 from NIH to G.F.J.H.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Department of
Genetics, Washington University School of Medicine, Box 8232, 660 South Euclid Ave., St. Louis, MO 63110. Phone: (314) 747-1808. Fax: (314)
362-7855. E-mail: chardy{at}genetics.wustl.edu.
 |
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