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Vol. 10, Issue 12, 4043-4057, December 1999
The Salk Institute for Biological Studies, Molecular Biology and Virology Laboratory, La Jolla, California 92037
Submitted June 18, 1999; Accepted September 27, 1999| |
ABSTRACT |
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The minichromosome maintenance (MCM) proteins MCM2-MCM7 are conserved eukaryotic replication factors that assemble in a heterohexameric complex. In fission yeast, these proteins are nuclear throughout the cell cycle. In studying the mechanism that regulates assembly of the MCM complex, we analyzed the cis and trans elements required for nuclear localization of a single subunit, Mcm2p. Mutation of any single mcm gene leads to redistribution of wild-type MCM subunits to the cytoplasm, and this redistribution depends on an active nuclear export system. We identified the nuclear localization signal sequences of Mcm2p and showed that these are required for nuclear targeting of other MCM subunits. In turn, Mcm2p must associate with other MCM proteins for its proper localization; nuclear localization of MCM proteins thus requires assembly of MCM proteins in a complex. We suggest that coupling complex assembly to nuclear targeting and retention ensures that only intact heterohexameric MCM complexes remain nuclear.
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INTRODUCTION |
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The minichromosome maintenance (MCM) proteins are a family of
essential eukaryotic replication proteins with six distinct members
(MCM2-MCM7) (reviewed by Chong et al., 1996
; Romanowski and
Madine, 1996
; Kearsey and Labib, 1998
). Initially identified in
Saccharomyces cerevisiae, they have been characterized in a wide variety of eukaryotes, including human, mouse, Xenopus,
Drosophila, and Arabidopsis, as well as in the
fission yeast Schizosaccharomyces pombe. The MCM proteins
are essential for the initiation of replication and normal S phase
progression. Although closely related, each MCM protein is essential
for viability. This suggests that they contribute unique activities to
their common function.
The MCM proteins form heteromeric complexes with the proteins in
a 1:1 stoichiometry (reviewed by Kearsey and Labib, 1998
). The
hexameric complex is apparently composed of a subcomplex consisting of
a tightly associated core complex (MCM4/6/7) that is loosely associated
with MCM2 and a more loosely associated subcomplex, the peripheral
dimer (MCM3/5) (Table 1) (Burkhart
et al., 1995
; Kimura et al., 1996
; Schulte
et al., 1996
; Adachi et al., 1997
; Kubota
et al., 1997
; Thommes et al., 1997
; Sherman and
Forsburg, 1998
; Sherman et al., 1998
). Although the precise
molecular function of the MCM protein complex remains to be determined,
a recent report showed weak ATPase and DNA helicase activities in the
core complex of human MCM4/6/7 (Ishimi, 1997
), which may be regulated by MCM2 (Ishimi et al., 1998
). To identify the
cis and trans factors required for complex
assembly, we have examined in detail a single fission yeast subunit,
Mcm2p (encoded by the cdc19+ gene).
Previously, we carried out an extensive mutational analysis of the
protein to define its functional domains (Forsburg et al., 1997
). Using our panel of mutant derivatives, we used
coimmunoprecipitation analyses to demonstrate that multiple regions of
Mcm2p are required for its association with other proteins in the MCM
complex (Sherman et al., 1998
). In this study, we
investigate a mechanism for regulating the assembly of the functional
hexameric MCM complex in the nucleus.
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MCM proteins are located in the nucleus throughout the cell cycle in
most organisms (reviewed by Kearsey and Labib, 1998
). The exception is
the budding yeast S. cerevisiae, in which most MCM proteins
exhibit cell cycle-regulated nuclear localization and are found in the
nucleus only during G1 and S phase; one recent report disputes this
(Hennessy et al., 1990
; Yan et al., 1993
; Dalton
and Whitbread, 1995
; Young et al., 1997
; Young and Tye, 1997
). However, the MCM proteins in mammalian, Xenopus, and
Drosophila systems remain in the nucleus throughout
interphase, although intranuclear distribution changes. The proteins
are chromatin associated in late mitosis but are displaced
progressively during S phase. Chromatin association appears to
correlate with the phosphorylation state of the MCM proteins (reviewed
by Kearsey and Labib, 1998
).
In fission yeast, all six MCM proteins are constitutively in the
nucleus (Maiorano et al., 1996
; Okishio et al.,
1996
; Sherman and Forsburg, 1998
; this work; Liang and Forsburg,
unpublished data), as are their metazoan homologues. In the current
study, we present evidence demonstrating for the first time that this nuclear localization depends on the assembly of an intact hexameric MCM
complex. We show that nuclear localization of wild-type MCM proteins is
disrupted in mcm mutant strains, suggesting that
localization of each MCM protein depends on the other MCM proteins. Our
data further suggest that wild-type MCM subunits are actively exported from the nucleus when MCM function is abrogated. Focusing on the Mcm2p
subunit, we show that mutant Mcm2 proteins defective in binding to
other MCM proteins are also defective for nuclear localization but that
the NLS-defective mutant Mcm2p is still capable of binding other MCM
proteins. Interestingly, the NLS sequences we define in Mcm2p are
necessary but not sufficient for its localization. We propose that MCM
protein localization requires both targeting to and retention in the
nucleus and that these events require assembly of an MCM complex.
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MATERIALS AND METHODS |
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Yeast Strains and Media
Yeast cultures were grown in rich (yeast extract with
supplements) or Edinburgh minimal medium supplemented with leucine, adenine, and uracil as needed at 25°C unless indicated otherwise (Moreno et al., 1991
). Culture medium was purchased from
Difco Laboratories (Detroit, MI). Repression of the nmt
promoter was maintained by addition of thiamine to 15 µM. For
monitoring the localization of mutant Mcm2 proteins, low-level
expression was induced by growing cells in selective medium
supplemented with 0.05 µM thiamine for 20 h (Javerzat et
al., 1996
). For monitoring the localization of the chimeric
jellyfish green fluorescent protein and
-galactosidase fusion
protein (GFP-
gal), cells were induced for expression in the absence
of thiamine for 24 h at 25°C. Congenic S. pombe
strains were originally derived from the strain 972 (h
). The fission yeast strains used
in this study are listed in Table 2.
Strains FY831, FY832, FY835, FY836, FY837, and FY979 were generated by
crossing the temperature-sensitive mutants to FY798. The
mis5-268 allele used to construct FY979 and FY961, and the
crm1-809 allele used to construct FY894 and FY1102, were a
gift from M. Yanagida (Kyoto University, Kyoto, Japan). The crm1-11R allele used to construct strains FY1139 and FY1152
was a gift from T. Toda (Imperial Cancer Research Fund
Laboratories, London, United Kingdom). NLS reporter strains were
generated by transformation of the wild-type fission yeast strain FY6
with each GFP-lacZ integrating plasmid digested with
NruI to target integration to the leu1 locus.
Stable integration in Leu+ prototrophs was
confirmed by random spore analysis. Plasmids pSGP581 (no NLS), pSGP583
(SV40 NLS), pSGP584 (mutant SV40 NLS), pSGP585 (NLS1), pSGP586
(NLS2), and pSGP587 (NLS1-M9) were integrated to generate the strains
FY838 (no NLS), FY840 (SV40 NLS), FY841 (mutant SV40 NLS), FY842
(NLS1), FY843 (NLS2), and FY844 (NLS1-M9). The strain FY1023 was
constructed by digesting the pJK148-derived vector containing the
triple hemagglutinin (HA) epitope tag fused to the carboxy terminus of
Mcm3p (pDS97) with SphI and integrating it into a wild-type
fission yeast diploid. Leu+ diploids were
sporulated to obtain Leu+ haploid prototrophs.
Leu+ haploids were cold sensitive (restrictive
temperature, 17°C). Backcross of the Leu+
haploid to Leu
confirmed linkage of the
cold-sensitive phenotype to the Leu+ marker.
Genomic mcm3+ rescued the cold-sensitive
phenotype. Double mutant strains FY1100, FY1101, FY1102, FY1139, and
FY1152 were all constructed by tetrad dissection. Double mutant
cdc19-P1 mcm3-HA was a rare segregant. In tetrad analysis,
most double mutants arrested as microcolonies with 12-40 cells, with
some cells elongated. The cdc19-P1 mcm3-HA strain we
recovered contains an uncharacterized suppressor of the cold-sensitive
phenotype of mcm3-HA. The strain behaves similarly to
cdc19-P1 mcm3+.
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Plasmid DNA Construction
Restriction enzymes and DNA-modifying enzymes were purchased
from New England Biolabs (Beverly, MA). A GFP-lacZ reporter
vector, pSGP502, allows insertion of a test NLS cassette at the amino terminus of GFP-
gal. pSGP500 (leu1+,
ars1, lacZ) contains ars1 as a
1.2-kilobase (kb) EcoRI/end-filled fragment cloned into
NotI/end-filled pSLF107 (lacZ gene cloned into
pJK148-derived vector) (Forsburg, 1993
; Keeney and Boeke, 1994
).
pSGP501 (leu1+, ars1,
GFP-lacZ with no NLS) contains the nmt promoter
and GFP gene (Haseloff et al., 1997
) from pSGP573
as a 2-kb PstI/BglII (blunt) fragment placed
upstream and in frame with lacZ of pSGP500 digested with
PstI/SalI (end filled). pSGP502
(leu1+, ars1,
GFP-lacZ with no initiation ATG, unique KpnI
site) was constructed by swapping the nmt promoter and the
part of GFP from pSGP572K (GFP carboxy-terminal tagging
vector with unique KpnI site at the amino terminus of GFP)
as a 1.3-kb PstI/MscI fragment. Thus, pSGP502 can
be used to assay the functionality of a putative NLS by subcloning the
test NLS with its own initiation ATG into the unique KpnI
site in frame with the GFP-lacZ fusion. pSGP572 and pSGP573
are GFP-tagging vectors (Sherman, Pasion, and Forsburg, unpublished data).
Various NLS sequences were assayed by insertion at the
KpnI site. The NLS linker fragments were constructed by
annealing pairs of oligonucleotides. The SV40 NLS (SV40 large T antigen
residues 126-132, MAPKKKRKV) was constructed by annealing
oligonucleotides 147 (5'ACCATGGCTCCTAAGAAGAAGCGTAAGGTTGTAC3') and 148 (5'AACCTTACGCTTCTTCTTAGGAGCCATGGTGTAC3'). Mutant SV40 NLS
(MAPKEKDKV) was constructed by annealing
oligonucleotides 149 (5'ACCATGGCTCCTAAGGAGAAGGACAAGGTTGTAC3') and 150 (5'AACCTTGTCCTTCTCCTTAGGAGCCA-TGGTGTAC3'). NLS1
(Mcm2p residues 5-10, MARKRGRR) was constructed by annealing oligonucleotides 151 (5'ACCATGGCTCGGAAAAGGGGTCGCCGCGTAC3') and 152 (5'GCGGCGACCCCT-TTTCCGAGCCATGGTGTAC3'). The NLS1-M9
(MARKEGDR) was constructed by annealing
oligonucleotides 153 (5'ACCATGGCTCGGAAAGAGGGTGACCGCGTAC3') and 154 (5'GCGGTCACCCTCT-TTCCGAGCCATGGTGTAC3'). NLS2 (Mcm2p
residues 114-118, MARLRRR) was constructed by annealing
oligonucleotides 155 (5'ACCATGGCTAGGTTGAGACGACGTGTAC3') and 156 (5'ACGTCGTC-TCAACCTAGCCATGGTGTAC3'). Subcloning of each
NLS linker into pSGP502 digested with KpnI generated pSGP503
(SV40 NLS), pSGP504 (mutant SV40 NLS), pSGP505 (NLS1), pSGP506 (NLS2),
and pSGP507 (NLS1-M9). To integrate each reporter construct into
fission yeast, each GFP-lacZ sequence was subcloned as a
PstI/NruI fragment into the integrating vector pJK148 (Keeney and Boeke, 1994
) to generate the plasmids pSGP581 (no
NLS, derived from pSGP501), pSGP583 (SV40 NLS), pSGP584 (mutant SV40
NLS), pSGP585 (NLS1), pSGP586 (NLS2), and pSGP587 (NLS1-M9).
The Mcm2p expression vectors pSLF176, pSLF196 series, and pDS196 series
were described previously (Forsburg et al., 1997
). To
construct fission yeast vectors that expressed Mcm2p-M9 with the
wild-type or mutant SV40 NLS on the amino terminus, we constructed the
Mcm2p-M9 expression vectors pSGP86-M9 and pSGP96-M9. A KpnI linker was inserted at the unique SalI site of pSLF187-M9
(Forsburg et al., 1997
) and at the unique XhoI
site of the HA-tagging vector pSLF172 (Forsburg and Sherman, 1997
) to
generate pSGP187K-M9 and pSLF172K. The fragment encoding Mcm2p-M9 was
subcloned from pSGP187K-M9 as a 3-kb KpnI/NotI
fragment into pSLF172K digested with KpnI/NotI to
generate pSGP187-M9. Either the wild-type SV40 NLS (oligonucleotides 147/148) or mutant SV40 NLS (oligonucleotides 149/150) was ligated into
pSGP187-M9 digested with KpnI to generate pSGP86-M9 or
pSGP96-M9, respectively. To express wild-type Mcm2p or NLS mutant
Mcm2p-M9, we constructed pSGP56 and pSGP56-M9, which are essentially
pSLF176 and pSLF196-M9 lacking the HA epitope. The 0.7-kb
BglII/SmaI fragment (carboxy terminus of Mcm2p
with no HA epitope) was subcloned from pSLF167 into
BglII/SmaI-digested pSLF176 or pSLF196-M9 to
generate pSGP56 and pSGP56-M9. pSLF167 contains the
cdc19+ cDNA (Forsburg et al.,
1997
).
Antibodies and Immunofluorescence Analysis
For immunofluorescence, anti-HA antibody was used at a 1:2500
dilution (mAb 16B12; BAbCO, Richmond, CA) and affinity-purified anti-Mcm4/Cdc21p and anti-Mcm6/Mis5p (Sherman et al., 1998
)
were used at a 1:500 dilution. Secondary antibodies (donkey anti-mouse immunoglobulin G-Cy3 and donkey anti-rabbit immunoglobulin G-Cy3; Jackson Immunoresearch Laboratories, West Grove, PA) for
immunofluorescence were used at a 1:250 dilution.
The immunofluorescence protocol was basically as described (Demeter
et al., 1995
) with a modification in cell wall digestion: 0.2 mg of Novozyme 234 (BiosPacific, Emeryville, CA) and 0.5 mg of
Zymolyase 20T (Seikagaku, Tokyo, Japan) per milliliter of buffer for
5-7 min at 25°C. For the double mutant strains FY1139 and FY1152,
cells were digested for 15 min. DNA was stained with DAPI. For
photography, cells were briefly heat fixed onto microscope slides and
mounted in 4 µl of antifade (1 mg of
p-phenylenediamine per milliliter of glycerol) and covered
with glass coverslips. Microscopy was performed with a Leitz
Laborlux S microscope (Leica, Wetzlar, Germany). Images were captured
on Kodak (Rochester, NY) Ektachrome 400 film or on a SPOT2
charge-coupled device digital camera (Diagnostics Instruments, Sterling
Heights, MI) directly into Adobe (Mountain View, CA) Photoshop. Slides
were scanned by a Nikon (Garden City, NY) slide scanner.
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RESULTS |
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MCM Protein Localization Is Compromised in mcm Mutants
Fission yeast has six MCM proteins found in the nucleus throughout
the cell cycle. For simplicity, we will refer to each protein by its
MCM family name rather than by its gene name in this report (Table 1).
We monitored their cellular localization using indirect immunofluorescence analyses. Endogenous Mcm2p and Mcm3p were tagged at
the carboxy terminus with a triple HA epitope and detected with anti-HA
antibody. We detected Mcm4p and Mcm6p with affinity-purified polyclonal
antibodies (Sherman et al., 1998
). Figure
1A verifies that our reagents give
results consistent with previous reports and also shows that Mcm6p is
nuclear at all stages of the cell cycle (Maiorano et al.,
1996
; Okishio et al., 1996
; Sherman and Forsburg, 1998
).
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Mcm2p localization was disrupted in mcm mutant strains. At
the restrictive temperature, Mcm2p nuclear localization diminished and
cytoplasmic staining increased in both the cdc21ts and
mis5ts strains (Figure 1, Bi and Bii). This is not simply a
result of blocking cells in S phase, because there is no effect on
Mcm2p localization in other S phase mutants with defects in the
S. pombe origin recognition complex (orp1-4),
ribonucleotide reductase (cdc22-M45), DNA polymerase
(pol1-1), or DNA ligase (cdc17-K42) (Figure 1,
Biii-Bvi). Mutants causing cell cycle arrest at start (cdc10-V50) or G2/M (cdc25-22) similarly had no
effect on Mcm2p localization (our unpublished results). Thus, Mcm2p
nuclear localization depends on other MCM proteins.
A reciprocal experiment showed that the localization of wild-type MCM proteins was affected in a cdc19 temperature-sensitive strain. At the restrictive temperature, Mcm3p, Mcm4p, and Mcm6p nuclear localization was strikingly decreased and cytoplasmic staining was increased (Figure 1C). Thus, not only does Mcm2p localization require other MCM proteins, but localization of other MCM proteins requires Mcm2p.
We completed our analysis by assessing the localization of multiple MCM
proteins in different mcm mutant backgrounds (Table 3A; Figure 1, B and C). At the
nonpermissive temperature for each mcm mutant strain, every
wild-type MCM protein analyzed demonstrated an increase in cytoplasmic
staining and a decrease in nuclear staining. Together, these results
are consistent with each MCM protein depending on other MCM subunits
for appropriate nuclear localization. We next examined whether these
phenotypes reflected defects in targeting, in retention, or both.
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MCM Proteins Are Actively Exported from the Nucleus
The loss of the wild-type MCM proteins from the nucleus in
mcm temperature-sensitive strains could reflect protein
turnover and failure to import newly synthesized molecules, or it could indicate a defect in protein retention in the nucleus. Previously, we
reported that steady-state levels of wild-type MCM proteins are
unchanged in cells arrested by mcm temperature-sensitive
mutations, even though assembly of the MCM complex is disrupted
(Sherman et al., 1998
). Because there is no evidence for any
changes in protein level, we examined the role of nuclear export in
redistribution of MCM proteins in wild-type and mcm mutant
cells. The crm1+ gene encodes a nuclear
export receptor (Fukuda et al., 1997
). To determine whether
MCM relocalization requires active nuclear export, we simultaneously
inactivated crm1 and the MCM complex. If MCM proteins
require crm1-dependent active export, they should be trapped
in the nucleus under these restrictive conditions.
We used two crm1 alleles for this experiment. First, we
combined a cold-sensitive allele of crm1
(crm1-809) (Nishi et al., 1994
; Kudo et
al., 1997
) and a cold-sensitive allele of mcm3
(mcm3-HA). Fortuitously, the carboxy-terminal HA epitope tag
on Mcm3p confers cold sensitivity (Figure
2A); the cells arrest with a
cdc phenotype and a 2C DNA content (our unpublished results)
typical of other mcm conditional mutants (Coxon et
al., 1992
; Miyake et al., 1993
; Forsburg and Nurse,
1994
; Takahashi et al., 1994
). Interestingly, Mcm3p-HA
itself remains in the nucleus at the restrictive temperature (Figure
2B). The same effect has been observed for other cold-sensitive MCM
proteins, accompanied by enhanced detection by immunofluorescence (Okishio et al., 1996
). However, Mcm3p-HA is able to exit
the nucleus under some conditions because it is redistributed in
cdc19 and cdc21 temperature-sensitive strains
grown at 36°C (Table 3B). Consistent with our observations for all
the other mutant mcm strains, arrest of cold-sensitive
mcm3-HA at 17°C resulted in redistribution of wild-type
MCM proteins to the cytoplasm (Figure 2C; Table 3B). In the double
mutant crm1-809 mcm3-HA, the wild-type MCM proteins remained
in the nucleus instead of accumulating in the cytoplasm after
incubation at 17°C (Figure 2D; Table 3B).
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Next, we combined a temperature-sensitive allele of crm1
(crm1-11R) (Kumada et al., 1996
) with the
temperature-sensitive allele of mcm2 (cdc19-P1).
The results were the same: the wild-type MCM proteins now remained
nuclear (Figure 2D; Table 3A). These results suggest that an active
nuclear export system is required for relocalization of the MCM
proteins when a single subunit is inactivated. Together, these data are
consistent with a model in which localization of any one MCM protein is
influenced by the activity of all other members of the complex. When
MCM function is abrogated, the wild-type MCM subunits are removed from
the nucleus via an active nuclear export system.
Nuclear Localization of Mcm2p Requires Multiple Domains
The only fission yeast MCM proteins reported to have identifiable
nuclear localization signals are Mcm2p and Mcm3p (Forsburg and Nurse,
1994
; Sherman and Forsburg, 1998
). Mcm2p has two sequences with
homology to the SV40 NLS (Kalderon et al., 1984b
): Mcm2p residues 5-10 (RKRGRR), designated NLS1, and residues 114-118 (RLRRR), designated NLS2 (Forsburg and Nurse, 1994
). Nuclear
localization signals of this type have been characterized in several
other fission yeast proteins (Shiozaki and Yanagida, 1992
; Birkenbihl and Subramani, 1995
; Bouvier and Baldacci, 1995
). In addition, there
are two potential nuclear export sequences (NESs) (reviewed by Kim
et al., 1996
; Nakielny and Dreyfuss, 1997
; Mattaj and
Englmeier, 1998
) at amino acid residues 627-638 (IVTTLQARCTII) and
771-780 (VRHLESAIRL). We have previously analyzed point mutations and sequence deletions in these regions of Mcm2p for their effect on
complementation (Forsburg et al., 1997
) and complex assembly (Figure 3K; Table
4) (Sherman et al., 1998
). We
used indirect immunofluorescence to determine the effect of these
mutations on Mcm2p localization. Wild-type and mutant proteins were
expressed at low levels in wild-type cells under the control of the
thiamine-regulatable nmt promoter. Each mutant protein was
tagged with an HA epitope at the carboxy terminus, which allowed the
episomally encoded protein to be distinguished from the endogenous
wild-type Mcm2p. The epitope tag itself has no effect on normal Mcm2p
function or localization in a wild-type strain background (Forsburg
et al., 1997
).
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Wild-type HA-tagged Mcm2p expressed at low levels from the plasmid
(Figure 3A) showed similar localization to that seen with Mcm2p-HA
integrated under its own promoter (Figure 1A), although with a slightly
higher cytoplasmic background. However, when the promoter was fully
induced and expression was ~100-fold that of endogenous Mcm2p
(Forsburg et al., 1997
), the cells stained heavily throughout the cytoplasm for Mcm2p-HA and the nuclei appeared dark
(Figure 3B). Interestingly, this overproduction has no toxic effect
(Forsburg et al., 1997
). That excess Mcm2p accumulates in
the cytoplasm suggests that there may be some mechanism or limiting
factor regulating the level of free Mcm2p in the nucleus. The phenotype
of Mcm2p overexpression in wild-type cells contrasts with the phenotype
of Mcm4p overproduction, which is toxic and results in the
accumulation of spots or aggregates of Mcm4p in the cytoplasm (Maiorano
et al., 1996
; Forsburg et al., 1997
).
Using this episomal expression assay, we tested our panel of mutant
Mcm2 proteins for defects in localization. The results of this assay
are shown in Figure 3 and summarized in Table 4. Only functional
versions of Mcm2p (wild type or mutants with small amino-terminal
deletions) were clearly detected as nuclear proteins (Figure 3, A and
G) (our unpublished results). These proteins are all able to complement
cdc19-P1 and form MCM complexes with wild-type affinity, as
assayed previously by coimmunoprecipitation analyses (Forsburg et
al., 1997
; Sherman et al., 1998
). Mcm2p-M6 and Mcm2p-M7
(NTP-binding site mutant; Figure 3D) (our unpublished results) showed
weak nuclear localization. These proteins have mutations in the same
residue and have weak MCM-binding ability; only Mcm2p-M7 can complement
(Forsburg et al., 1997
; Sherman et al., 1998
).
The remaining mutant proteins all showed widespread cytoplasmic
staining and failed to accumulate in the nucleus. In general,
functional Mcm2p mutants were able to localize properly, whereas
mutants that failed to complement cdc19ts also failed to
localize to the nucleus.
When we correlated nuclear localization to binding and complementation
data, the noncomplementing cytoplasmic mutants fell into two classes.
The majority of these were defective not only in nuclear localization
but also in MCM complex assembly (Table 4) (Forsburg et al.,
1997
; Sherman et al., 1998
). These included most mutations
constructed throughout the Mcm2 protein (Table 4; Figure 3) (our
unpublished results): the zinc finger mutants Mcm2p-M1, -M2, -M3, and
-M4 (Figure 3C) (our unpublished results); the carboxy-terminal
truncation Mcm2p-D6 (Figure 3H); the large amino-terminal truncation
Mcm2p-D7 (Figure 3I); and the deletions spanning the MCM core homology
domain, Mcm2p-D8, -D9, and -D10 (Figure 3J) (our unpublished results).
Thus, in most cases, mutations that result in defective MCM protein
interaction also disrupt Mcm2p nuclear localization.
However, two mutant proteins retained the ability to bind other
MCM proteins but remained cytoplasmic (Figure 3, E and F) (Forsburg
et al., 1997
; Sherman et al., 1998
). Mcm2p-M9 and
Mcm2p-M10 contain mutations in the two putative NLS elements. Thus,
under some conditions, binding of Mcm2p to other MCM proteins can be uncoupled from nuclear localization. We further characterized these
mutant proteins to determine whether they define true NLS sequences and
used them as tools to determine whether Mcm2p binds other MCM proteins
in the cytoplasm.
NLS1 Is a Functional Fission Yeast NLS
The mutants Mcm2p-M9 and Mcm2p-M10 fail to localize properly,
suggesting that they define sequences necessary for nuclear localization. We asked whether these putative NLS elements are sufficient for nuclear localization. We fused NLS1 or NLS2 to a
chimeric GFP-
gal fusion protein. This reporter strategy has been
used successfully to assay NLS function in budding yeast (Lee et
al., 1996
; Yoon et al., 1997
). We integrated the
GFP-lacZ reporter gene at the leu1 locus in
fission yeast. For positive and negative controls, we fused the
reporter to the wild-type SV40 NLS, which has been shown to function in
fission yeast (Shiozaki and Yanagida, 1992
), and to a nonfunctional
mutant SV40 NLS (Kalderon et al., 1984a
). GFP-
gal
requires a functional NLS for nuclear localization (Figure
4B). Absence of an NLS or insertion of
the mutant SV40 NLS in place of the wild-type NLS generated a
cytoplasmic protein (Figure 4, A and C). We determined that the NLS1
sequence from Mcm2p also targets the reporter protein to the nucleus
(Figure 4D), whereas point mutations corresponding to Mcm2p-M9 disrupt NLS function in this reporter assay (Figure 4E). Thus, NLS1 fulfills the criteria for a bona fide nuclear localization sequence, being both
necessary and sufficient for nuclear targeting.
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Neither NLS2 nor the mutant NLS2-M10 was able to target the reporter to the nucleus (Figure 4F) (our unpublished results). In this protein context, the NLS2 sequence is insufficient for activity. It is possible that the NLS2 sequence as defined is incomplete and requires additional flanking sequence. The sequence is still necessary for localization of Mcm2p (Figure 3F), even though it is not sufficient for targeting a reporter protein.
Finally, we demonstrated that the only defect in Mcm2p-M9 is in nuclear
localization. When fused to the SV40 NLS, this protein was able to
complement cdc19ts and
cdc19 and was correctly
localized to the nucleus (Figure 5A) (our
unpublished results). There was no complementation when we used a
mutant derivative of SV40 NLS (Figure 5A) (our unpublished results).
Thus, the only defect in Mcm2p-M9 is its failure to localize to the
nucleus. Similar results were obtained for Mcm2p-M10 (our unpublished
results).
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MCM Subcomplexes Can Form in the Cytoplasm
Because Mcm2p-M9 and Mcm2p-M10 cannot localize to the nucleus
(Figure 3, E and F) but can associate with other MCM proteins (Sherman
et al., 1998
), we predicted that binding of Mcm2p to the
core complex (Mcm4/6/7) occurs in the cytoplasm at a step that precedes
nuclear import. To confirm this, we sought an in vivo assay independent
of immunoprecipitation analyses. We reasoned that if Mcm2p-M9 binds the
core complex in the cytoplasm, then increasing the dose of Mcm2p-M9
might trap wild-type MCM proteins in the cytoplasm. At sufficiently
high levels, this redistribution of wild-type MCM proteins should
inhibit growth as the MCM proteins become limiting in the nucleus.
Previously, we showed that overexpression of Mcm2p-M9 is not toxic in
wild-type cells but that overexpression of Mcm2p-M9 in
cdc19ts cells is lethal at the permissive temperature (Forsburg et al., 1997
). This "synthetic dosage
lethality" is also observed on overexpression of Mcm2p-M9 in the
double mutant cdc19-P1 mcm3-HA strain (Figure 5B). The
amount of Mcm2 temperature-sensitive protein is reduced in these
strains (Sherman et al., 1998
; Liang et al.,
1999
), and the protein has a reduced affinity for other MCM proteins
compared with wild-type Mcm2p (Sherman et al., 1998
). This
suggests that the Mcm2-M9 protein outcompetes the Mcm2
temperature-sensitive protein for binding to the wild-type MCM proteins
in this strain. If so, we predict that the wild-type MCM proteins
should be redistributed to the cytoplasm when Mcm2p-M9 is overproduced.
This proved to be correct. As shown in Figure 5C, the toxic phenotype associated with overproduction of Mcm2p-M9 in cdc19-P1 mcm3-HA is indeed accompanied by redistribution of wild-type MCM proteins to the cytoplasm. Localization is normal in strains overproducing wild-type Mcm2p (Figure 5, Ci-Ciii). However, cells overproducing Mcm2p-M9 were elongated and unable to form colonies, accumulating a 2C DNA content (our unpublished results). Nuclear immunofluorescence of the core complex components Mcm4p and Mcm6p was significantly reduced, and cytoplasmic immunofluorescence was increased (Figure 5, Civ-Cvi). In addition, overexpression of Mcm2p-M9 also disrupted the localization of the peripheral dimer component Mcm3p-HA. Even at low levels of expression of Mcm2p-M9, endogenous Mcm4p nuclear localization was compromised (our unpublished results). This not only indicates that MCM complexes can assemble in the cytoplasm but also suggests that the NLS defect of Mcm2p-M9 is sufficient to keep them there.
Mutant Mcm2 Proteins with an Intact NLS1 Fail to Accumulate in the Nucleus
These observations present us with a paradox. NLS1 is required for the normal localization of Mcm2p and is clearly sufficient to target a reporter protein to the nucleus. However, it is not sufficient to target Mcm2p; most Mcm2p mutants that are defective for both MCM binding and nuclear localization have an intact NLS1. The NLS mutants are defective for localization but retain the ability to bind other MCM proteins. In no case did we find a mutant that was able to localize to the nucleus but unable to associate with other MCM proteins. Therefore, we suggest that complex assembly precedes, and is required for, nuclear localization.
We reasoned that NLS1, and perhaps NLS2, is not functional in its native context unless Mcm2p is assembled in an MCM complex. If this is true, the mutant Mcm2/Cdc19 proteins should never enter the nucleus, despite the presence of an intact NLS1. Alternatively, they might enter the nucleus but be immediately exported because of a failure to assemble with other MCM proteins. To distinguish between these alternatives, we used the cold-sensitive crm1 strain to block nuclear export. If mutant Mcm2p derivatives are capable of nuclear import, they should be trapped in the nucleus in crm1 cells at the restrictive temperature.
crm1 cells expressing wild-type or mutant Mcm2 proteins were
incubated at the restrictive temperature for 6 h. Wild-type Mcm2p remained in the nucleus (Figure 6A). The
NLS mutants Mcm2p-M9 (Figure 6D) and Mcm2p-M10 (Figure 6E) and the
amino-terminal truncation Mcm2p-D7 (Figure 6G), which lacks both NLS1
and NLS2, were found in the cytoplasm. This is the expected result
because they lack functional targeting sequences. We tested two
deletion mutants, Mcm2p-D6 and Mcm2p-D10, and a zinc finger point
mutant, Mcm2p-M2, each of which contains NLS1 and NLS2 but fails to
associate with other MCM proteins. In the nuclear export-defective
strain, Mcm2p-D6 remained cytoplasmic (Figure 6F). This mutant protein
is a carboxy-terminal truncation (Table 4). Similar cytoplasmic
localization was observed for Mcm2p-M2 (Figure 6C). This result
suggests that mutant Mcm2/Cdc19 proteins that are unable to associate
with other MCM proteins are not imported into the nucleus despite the
presence of NLS1 and NLS2. This is consistent with subcomplex assembly
being required for Mcm2p NLS function.
|
Interestingly, Mcm2p-D10 did accumulate in the nucleus in ~10% of crm1 cells (Figure 6H). This mutant protein contains a large deletion in the MCM core domain and is a cytoplasmic protein when expressed in a wild-type strain. We also examined the localization of excess wild-type Mcm2p in the crm1 mutant strain. In wild-type cells, Mcm2p accumulated in the cytoplasm when overproduced. If it were shuttling in and out of the nucleus, we would expect the protein to accumulate in the nucleus in a crm1 mutant that blocks export. However, this was not observed (Figure 6B).
| |
DISCUSSION |
|---|
|
|
|---|
In fission yeast and metazoa, the conserved MCM proteins are found in the nucleus throughout the cell cycle. We have examined the localization of MCM proteins in fission yeast and found that there is a role for the nuclear envelope in regulating these proteins even though their localization is not cell cycle dependent: it serves to maintain intact hexameric MCM complexes inside the nucleus. We propose that the nuclear targeting of Mcm2p and associated proteins requires assembly of the MCM proteins to activate the Mcm2p NLS. In contrast, when Mcm2p is not associated with other MCM proteins in the nucleus, the NLS is inaccessible and the protein is exported. Thus, assembly of an intact hexameric MCM complex is linked to the nuclear localization of individual MCM subunits.
An attractive model is that the association of at least the core MCM
proteins (MCM4/6/7) and MCM2 in the cytoplasm is required for their
targeting of the subcomplex to the nucleus (Figure
7). Previously, we and others have shown
that the MCM heterohexamer contains subcomplexes: a core of MCM4/6/7
bound by MCM2 and a peripheral dimer of MCM3/5 (Ishimi et
al., 1996
; Kimura et al., 1996
; Adachi et
al., 1997
; Kubota et al., 1997
; Thommes et
al., 1997
; Sherman and Forsburg, 1998
; Sherman et al.,
1998
). That coassembly of subcomplexes of MCM proteins occurs in the
cytoplasm is demonstrated by the ability of the NLS1 mutant, Mcm2p-M9,
to trap wild-type MCM proteins in the cytoplasm. In fission yeast, as
in budding yeast, only Mcm2p and Mcm3p homologues have consensus nuclear localization sequences. Thus, Mcm3p may similarly target Mcm5p
to the nucleus. In this model, retention of all six MCM proteins in the
nucleus would require binding of the peripheral dimer MCM3/5 to the
subcomplex MCM2/4/6/7 to inactivate NESs. The disruption of Mcm3p
localization in the cdc19 mutant and the disruption of MCM
core complex localization in the mcm3 mutant may indicate
that assembly of the full hexameric complex is required for nuclear
retention. Alternatively, the intact complex might assemble in the
cytoplasm and require both sets of NLSs to target the hexamer to the
nucleus.
|
This model linking hexameric MCM complex assembly and nuclear
localization in fission yeast is based on three major observations. First, MCM protein localization is interdependent: in mcm
temperature-sensitive strains, the wild-type MCM proteins are lost from
the nucleus at the restrictive temperature. MCM protein associations
are also disrupted under these conditions (Sherman et al.,
1998
). In either the mcm3-HA cold-sensitive or the
cdc19 temperature-sensitive mutant, this redistribution of
MCM proteins requires an active nuclear export system. It remains to be
determined if each MCM protein contains an NES, whether MCM
subcomplexes or individual subunits are targets for export, or if
export depends on interaction with an NES-containing protein. There are
potential NESs in Mcm2p at residues 627-638 and 771-780, based on
comparison with consensus NESs (Kim et al., 1996
; Nakielny
and Dreyfuss, 1997
; Nigg, 1997
; Mattaj and Englmeier, 1998
). Notably,
Mcm2p-D10 retains the putative NES at residues 771-780 (Table 4) and
can be trapped in the nucleus in the nuclear export-defective strain.
Masking of the NES has been proposed as a mechanism for regulating p53
subcellular localization (Stommel et al., 1999
).
Tetramerization of p53 monomers blocks the NES elements, resulting in
nuclear retention of the p53 complex.
Second, using a panel of mutations in Mcm2p, we show that mutants that
disrupt complementation and MCM protein interactions (Forsburg et
al., 1997
; Sherman et al., 1998
) also abolish nuclear localization, even in the presence of an intact NLS. Trivially, this
could suggest that all mutant proteins fail to fold properly, even
though they are all produced and stable (Forsburg et al., 1997
; Sherman et al., 1998
). However, several observations
argue against this. (1) The NLS2 mutant Mcm2p-M10 also contains an
intact NLS1, yet it fails to accumulate in the nucleus. In this case, however, the protein is still able to bind other MCM proteins (Sherman
et al., 1998
) and can be rescued by adding a heterologous NLS, which suggests that its structure is still intact. (2) The protein
tolerates deletions in the amino terminus (D1, D2, D3) that do not
affect binding, localization, or complementation. (3) A mutation in the
putative nucleotide-binding site, M7 (K540R), also produces a
functional protein; an alanine mutation of the same lysine residue
disrupts activity. Both mutant proteins exhibit reduced MCM protein
binding and nuclear localization. These observations demonstrate that
the protein can accommodate both point and deletion mutations. (4)
Among the nearly 20 other mutant proteins with point and deletion
mutations throughout the protein, all are produced and stable; none
shows nuclear localization, despite the presence of NLS1 and NLS2.
Although one can never prove that these proteins are folded normally,
indirect evidence suggests that at least some of them are intact. We
suggest that they are specifically deficient in targeting. An
intriguing reason is that the NLS remains masked because the mutant
proteins fail to interact with other MCM proteins. We also observed
that overproduced Mcm2p does not accumulate in the nucleus in wild-type
or crm1 mutant cells. This result suggests that some factor
is limiting for either its import or its retention. This is unlikely to
be attributable to an effect on general import machinery because
overexpression of wild-type Mcm2p has no deleterious phenotype. Because
we never observed nuclear localization without MCM binding, we deduce
that binding is required for localization.
Our third major observation is based on analysis of Mcm2p NLS
sequences. Mcm2p contains at least one NLS (NLS1) that is sufficient to
target a reporter protein to the nucleus, but that sequence is
insufficient to target binding-defective Mcm2p mutants to the nucleus.
Nor can NLS1 target an NLS2 mutant Mcm2p to the nucleus, even though
its ability to assemble with other MCM proteins is normal. Mutations in
either NLS have no effect on complex assembly (Sherman et
al., 1998
) but abolish localization; this localization can be
rescued by adding a heterologous NLS to the mutant protein. In
addition, NLS mutants can be used to sequester wild-type MCM proteins
in the cytoplasm. The NLS mutants allow us to uncouple complex assembly
from localization and suggest that complex assembly precedes
localization. Thus, we suggest that complex assembly is necessary but
not sufficient for localization of Mcm2p.
We infer that the NLS sequences are not active or exposed unless
Mcm2p is assembled with other MCM proteins. The Mcm2p-D10 mutant, which
contains a large deletion but retains NLS1 and NLS2, shows weak nuclear
localization in the crm1 mutant, suggesting that NLS masking
is defective for this mutant protein. One possible explanation for this
observation is that the large deletion in Mcm2p-D10 not only prevents
association of the mutant protein with other MCM proteins but also
prevents complete inactivation of NLS1 and NLS2. In the wild-type
strain, Mcm2p-D10 with partially active NLS function is inefficiently
imported, but the functional nuclear export mechanism removes the
mutant protein from the nucleus to the cytoplasm. In the
crm1 strain, Mcm2p-D10 is captured in the nucleus because of
the failure of the nuclear export system, but its nuclear localization
is substantially reduced compared with that of wild-type Mcm2p. There
is precedent for intramolecular masking of NLS function. Recently,
Humbert-Lan and Pieler (1999)
reported that a carboxy-terminal
transport regulatory domain may mask two NLS sequences in the
Xenopus B-Myb transcription factor, thus restricting B-Myb
to the cytoplasm. They propose that the domain acts via either
intramolecular or intermolecular interactions to regulate NLS function.
Because the Mcm2/Cdc19 NLS mutants can sequester the other MCM
proteins in the cytoplasm, and because localization of MCM subunits is
interdependent, we propose that Mcm2p may be required for import of
those MCM proteins that lack identifiable NLS elements. There have been
several recent reports that complex assembly allows nuclear targeting
of a protein that lacks a functional NLS. Piggyback mechanisms have
been proposed for the Fanconi anemia protein complex (Naf et
al., 1998
), mushroom homeodomain transcription factor complex
(Spit et al., 1998
), cytomegalovirus capsid assembly
(Plafker and Gibson, 1998
), mouse DNA primase (Mizuno et
al., 1996
), mammalian DNA repair enzymes (Boulikas, 1997
), STAT
proteins (Johnson et al., 1998a
,b
), and I
B (Turpin
et al., 1999
). Furthermore, two recent reports (Abu-Shaar
et al., 1999
; Berthelsen et al., 1999
) have
demonstrated that the subcellular localization of the
Drosophila homeodomain protein Extradenticle depends on
regulating the accessibility of its NLS and NES elements.
Heterodimerization of Extradenticle with Homothorax blocks NES
accessibility and leads to nuclear accumulation of the
Extradenticle/Homothorax complex. In each case, the cell assembles a
protein complex in the cytoplasm and then imports the complex into the
nucleus. The latter case provides an example of the role of nuclear
export in maintaining appropriate stoichiometry of complex subunits. In
this way, only active, intact complexes are present in the nucleus. Our
data suggest that fission yeast MCM complexes may also have this
spatial control of their assembly.
Such a mechanism may be conserved in other eukaryotes. Kimura and
colleagues (1996)
showed that overexpression of murine MCM6 and MCM5
led to their accumulation in the cytoplasm unless MCM2 and MCM3,
respectively, were coexpressed. In characterizing the NLS of budding
yeast Mcm3p, Young and colleagues (1997)
speculated that it may provide
nuclear access for other MCM proteins. Furthermore, Maiorano and
colleagues (1996)
suggested that the cytoplasmic accumulation of
overproduced fission yeast Mcm4p may indicate that Mcm4p depends on its
association with an NLS-containing limiting factor for its nuclear
import. Our interpretation is consistent with these data. It provides a
mechanism for the cell to assemble intact hexameric MCM complexes in
the nucleus and maintain the correct stoichiometry of the individual
subunits. By requiring the subcomplexes to assemble in the cytoplasm
before nuclear entry and actively exporting free MCM subunits or
subcomplexes from the nucleus, the cell avoids having unassociated MCM
proteins bind other factors or interfere with the function of the
intact MCM complex. Interestingly, this active nuclear export may
explain the shuttling behavior of MCM proteins reported in S. cerevisiae (Hennessy et al., 1990
; Yan et
al., 1993
; Dalton and Whitbread, 1995
; Young et al.,
1997
; Young and Tye, 1997
); uniquely in this organism, MCM proteins
leave the nucleus during S phase. This may indicate that the MCM
complex is normally disrupted during the cell cycle in this species.
Nuclear localization of MCM proteins thus appears to reflect a balance of nuclear import and export. Access to the requisite targeting sequences may be mediated by the interaction of the complex components or associated factors. Even though this localization is not cell cycle dependent in normal growth, it clearly imposes spatial regulation on the assembly and activation of these conserved proteins. We expect that such regulation will be a common feature of the assembly of complex protein structures in the nucleus.
| |
ACKNOWLEDGMENTS |
|---|
We thank Peter Doerner, Adan Colon-Carmona, and Jim Haseloff for the gift of the GFP vector (pGFP1.1), Mitsuhiro Yanagida for the mis5-268 and crm1-809 fission yeast strains, Tom Hope for assistance with nuclear export sequence analysis, Takashi Toda and Shelley Sazer for the crm1-11R strain, and Dan Sherman for the plasmid (pDS97) used in the construction of the mcm3-HA strain. We thank Mike McKeown, Tony Hunter, Martin Latterich, Tom Pollard, Dan Sherman, and Hilary Snaith for critical reading of the manuscript, and all Forsburg laboratory members for helpful discussions. This work was supported by American Cancer Society grant RPG-95-12-5-CCG to S.L.F., who is a Leukemia Society Scholar. S.G.P. received early support from National Institutes of Health grant CA-03970 and is a National Science Foundation Minority Postdoctoral Fellow.
| |
FOOTNOTES |
|---|
* Corresponding author: E-mail address: forsburg{at}salk.edu.
| |
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