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Molecular and Cellular Biology, April 1999, p. 2535-2546, Vol. 19, No. 4
Howard Hughes Medical
Institute2 and Department of Cell
Biology,1 Vanderbilt University School of
Medicine, Nashville, Tennessee 37232
Received 5 August 1998/Returned for modification 21 September
1998/Accepted 22 December 1998
The Schizosaccharomyces pombe dim1+ gene is
required for entry into mitosis and for chromosome segregation during
mitosis. To further understand dim1p function, we undertook a synthetic lethal screen with the temperature-sensitive dim1-35 mutant
and isolated lid (for lethal in dim1-35)
mutants. Here, we describe the temperature-sensitive lid1-6
mutant. At the restrictive temperature of 36°C, lid1-6
mutant cells arrest with a "cut" phenotype similar to that of
cut4 and cut9 mutants. An epitope-tagged
version of lid1p is a component of a multiprotein ~20S complex; the
presence of lid1p in this complex depends upon functional
cut9+. lid1p-myc coimmunoprecipitates with
several other proteins, including cut9p and nuc2p, and the presence of
cut9p in a 20S complex depends upon the activity of
lid1+. Further, lid1+
function is required for the multiubiquitination of cut2p, an anaphase-promoting complex or cyclosome (APC/C) target. Thus, lid1p is
a component of the S. pombe APC/C. In dim1
mutants, the abundances of lid1p and the APC/C complex decline
significantly, and the ubiquitination of an APC/C target is abolished.
These data suggest that at least one role of dim1p is to maintain or establish the steady-state level of the APC/C.
The cdc2 protein serine/threonine
kinase plays a key role in promoting cell cycle progression in all
eukaryotes (reviewed in references 30, 34, and
37). At the G2/M transition, cells enter
mitosis as a result of cdc2p activation, which in turn is dependent
upon the association of cdc2p with its positive regulatory partner,
cyclin B. The timed destruction of cyclin B at the end of mitosis is
one mechanism ensuring that cdc2p-cyclin B is inactivated in each cell cycle.
Indeed, the abrupt disappearance of cyclin observed at the end of each
cell cycle in fertilized sea urchin eggs first suggested the
possibility that cyclin destruction may be important for cell cycle
progression (10). The fact that nondegradable forms of cyclin B injected into frog egg cycling extracts prevented exit from
mitosis further strengthened this hypothesis (35). It has recently been demonstrated that although cyclin B is normally degraded
during mitosis in all eukaryotes to promote exit from mitosis (reviewed
in references 8, 17, and 26), at
least in budding yeast, the destruction of Clb2p, the major mitotic cyclin, is not absolutely required for cell cycle progression (42,
45).
Destruction of cyclins at mitosis occurs via ubiquitin-mediated
proteolysis (14), a multistep process in which a
ubiquitin-activating enzyme (E1) first activates ubiquitin by formation
of a high-energy thioester bond. E1 then transfers ubiquitin to an E2
or ubiquitin-conjugating enzyme. The E2 may transfer ubiquitin directly
to the substrate, targeting the substrate for destruction by the 26S
proteasome. Alternatively, the specificity of this reaction may be
determined by association of the E2 with a ubiquitin protein ligase
(E3) to catalyze ubiquitination of a target protein (reviewed in
references 7 and 19).
An E3 ubiquitin ligase that recognizes A- and B-type cyclins was
identified biochemically in clam and frog extracts and genetically in
fission and budding yeasts and is known as the anaphase-promoting complex or cyclosome (APC/C) (reviewed in references 8, 17, 26, and 44). The APC/C is a multisubunit
complex of ~20S that has been conserved throughout evolution
(reviewed in references 8, 17, 26, and
44). In Xenopus egg extracts, eight
components of the APC have been identified (27, 36), and the
sequences of their human homologs have been reported (50).
In Saccharomyces cerevisiae, 10 APC components have been
identified (22, 23, 29, 51-53). In
Schizosaccharomyces pombe, only four APC components have
been identified to date: cut4p (49), cut9p (40,
47), nuc2p (18, 28), and hcn1p (47). cut4p,
cut9p, and nuc2p are orthologs of S. cerevisiae Apc1p,
Cdc16p, and Cdc27p and of human APC1, APC6, and APC3, respectively.
hcn1p is related to S. cerevisiae Cdc26p and is apparently
important for APC/C activity only at elevated temperatures
(47). The cut4, cut9, and
nuc2 gene products interact physically, forming part of an
~20S complex (47, 49). Temperature-sensitive
cut4 and cut9 mutants all display a "cut"
phenotype at restrictive temperatures; in these mutants, chromosome
segregation and spindle elongation fail to occur, such that subsequent
cytokinesis bisects the nucleus or results in segregation of DNA to
only one daughter cell (40, 49).
The APC/C targets proteins containing a destruction box motif for
ubiquitin-dependent proteolysis during mitosis and G1
phases. While M phase cyclins were the first targets known, other APC/C target proteins have subsequently been identified. Anaphase chromosome segregation in the budding yeast S. cerevisiae requires
APC/C-mediated destruction of the nuclear protein Pds1 (9,
48), and in the fission yeast S. pombe, chromosome
segregation requires destruction of cut2p (12). Additional
substrates of the APC/C include the spindle component Ase1p
(24), cohesins (32), the Cdc5p "polo" kinase
(6, 43), and Cdc20p (43). In the absence of APC/C activity, spindle elongation, chromosome segregation, and exit from
mitosis are blocked.
Like components of the APC/C, dim1p also is required during mitosis for
chromosome segregation (5). dim1p is a highly conserved 17-kDa protein whose biochemical function is unknown. In S. cerevisiae, the ortholog of dim1+ was
originally called CDH1 (5), but the name has been
changed to DIB1. In an effort to further elucidate
dim1+ function, we undertook a synthetic lethal
screen with the temperature-sensitive dim1-35 mutant and
isolated lid (for lethal in dim1-35) mutants. Here, we describe the temperature-sensitive lid1-6 mutant.
At the restrictive temperature of 36°C, lid1-6 mutant
cells arrest with a cut phenotype similar to that of cut4
and cut9 mutants. An epitope-tagged version of lid1p
(lid1p-myc) is present in a high-molecular-weight complex of ~20S,
and the presence of lid1p in this complex depends upon functional
cut9p. Coimmunoprecipitation analyses demonstrate an in vivo
association among lid1p-myc and several other proteins, including cut9p
and nuc2p, and the presence of cut9p in a 20S complex depends upon the
activity of lid1p. Further, the multiubiquitination of cut2p depends
upon lid1+ function. Thus, lid1p is a component
of the S. pombe APC/C. To explain the genetic interaction
between dim1 and lid1 mutants, we have found that
the abundances of lid1p and the 20S APC/C complex are dependent upon
dim1+ function. Moreover, dim1
function is required for APC/C-mediated multiubiquitination of cut2p.
These data indicate that one role of dim1p in mitosis is to
establish or maintain the integrity and function of the APC/C.
Yeast methods, strains, and media.
The S. pombe
strains used in this study are listed in Table
1. Strains were grown in yeast extract
(YE) medium or minimal medium with appropriate supplements
(33). Crosses were performed on malt extract medium
(33) or glutamate medium (minimal medium lacking ammonium
chloride and containing 0.01 M glutamate, pH 5.6). Random spore
analysis and tetrad analysis were performed as described previously
(33). Double-mutant strains were constructed and identified
by tetrad analysis. Unless otherwise indicated, transformations were
performed by electroporation (38). Genomic DNA was isolated
as described previously (20, 33).
0270-7306/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.
The Schizosaccharomyces pombe
dim1+ Gene Interacts with the Anaphase-Promoting
Complex or Cyclosome (APC/C) Component lid1+ and
Is Required for APC/C Function
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ABSTRACT
Top
Abstract
Introduction
Materials and Methods
Results
Discussion
References
![]()
INTRODUCTION
Top
Abstract
Introduction
Materials and Methods
Results
Discussion
References
![]()
MATERIALS AND METHODS
Top
Abstract
Introduction
Materials and Methods
Results
Discussion
References
TABLE 1.
S. pombe strains used in this study
Plasmids and molecular biological techniques. All plasmid manipulations and bacterial transformations were by standard techniques (39). Essential features of plasmid construction are described below. All sequencing of plasmid DNA was performed by using Sequenase 2.0 (U.S. Biochemicals, Cleveland, Ohio) or Thermo Sequenase (Amersham Life Sciences, Cleveland, Ohio) according to the manufacturer's instructions. Unless otherwise specified, all PCRs were performed by using Taq DNA polymerase and the GeneAmp PCR reagent kit (Perkin-Elmer) in a PTC-100 Programmable Thermal Controller (MJ Research, Watertown, Mass.) programmed as follows: 94°C for 1 min, 50°C for 2 min, and 72°C for 2 min (40 cycles) and 72°C for 10 min. All [32P]dCTP-labeled probes for radioactive hybridization were labeled by using redivue [32P]dCTP (Amersham Life Sciences, Amersham, England) and the rediprime random primer labeling kit (Amersham Life Sciences) according to manufacturer's instructions.
dim1-35 synthetic lethal screen (lid screen). A dim1-35 strain carrying plasmid-borne mouse dim1 (mdim1) under control of the nmt1 promoter, pKG930 (5), was mutagenized with nitrosoguanidine as described previously (33). Approximately 85,000 mutagenized cells were plated at a density of 300 to 500 cells per plate on medium lacking thiamine in order to induce expression of mdim1. Plates were incubated at 25°C until colonies formed. Colonies were replica plated to medium containing thiamine in order to eliminate mdim1 activity. We used mdim1 for this screen because S. pombe dim1 activity under control of the nmt1 promoter was not effectively eliminated by the inclusion of thiamine in the medium, whereas mdim1 activity clearly was. Plates were incubated overnight at 25°C and then re-replica plated to medium containing thiamine. Plates were screened 2 days later for colonies that were inviable in the presence of thiamine.
Physiological experiments. For analysis of synchronous cell populations, 4 liters of cells was grown to mid-log phase (8 × 106 cells/ml) at the permissive temperature (25°C) in YE medium. Cells were separated on the basis of size by centrifugal elutriation in a Beckman JE 5.0 elutriator rotor. Cells synchronized in early G2 (the smallest cells in the population) were collected and inoculated into YE medium at 25 or 36°C. Synchrony was monitored at 20- to 25-min intervals by scoring 100 cells for the presence of a septum.
Flow cytometry and microscopy.
For flow cytometric analysis,
cells were fixed in ice-cold 70% ethanol, washed in 50 mM sodium
citrate, incubated with 0.1 mg of RNase A per ml in 50 mM sodium
citrate for 2 h at 37°C, and then stained with 1 µM Sytox
green in 50 mM sodium citrate for 1 h. Cells were sonicated and
analyzed by flow cytometry as described previously (41). All
fluorescence microscopy was performed on a Zeiss Axioskop with
appropriate filters. In order to visualize DNA, ethanol-fixed cells
were washed in phosphate-buffered saline and then stained with the
fluorescent DNA-binding dye DAPI (4',6-diamidino-2-phenylindole) at 1 µg/ml. For immunofluorescence, cells were fixed in 70% ethanol at
4°C, or in 100% methanol at
20°C, for 8 min and then washed with
phosphate-buffered saline and processed as described previously (2). For staining of microtubules, fixed cells were
incubated in a 1:10 dilution of the monoclonal TAT-1 primary antibody
(46) (a generous gift of K. Gull) followed by a 1:100
dilution of Texas red-conjugated goat antimouse secondary antibody
(Molecular Probes, Eugene, Oreg.).
Cloning and sequence analysis of lid1. lid1-6 mutant cells (KGY1150) transformed with a pUR19-based S. pombe genomic library (3) were selected at 25°C on medium lacking uracil and then replica plated to 36°C. Plasmids subsequently shown to be identical by restriction digestion and Southern blot analysis were recovered from two independent Lid1+ Ura+ colonies. Deletion constructs generated from the rescuing plasmid (pKG1030) were retransformed into lid1-6 cells in order to identify a minimal rescuing fragment. Sequencing of pKG1030 revealed that a portion of the insert was contained within c19g12 (21), a cosmid sequenced as part of the S. pombe genome sequencing project. The remainder of the insert was sequenced and, in combination with sequence obtained from c19g12, analyzed for coding potential.
For integration mapping, the complete 5.5-kb pKG1030 insert was subcloned into the S. pombe ura4-based integrating vector pJK210 (25) to generate pKG1025. pKG1025 was linearized at the unique SacI site within the insert, and the linearized plasmid was transformed into the lid1-6 ura4-D18 mutant strain KGY1150. Transformants were selected on medium lacking uracil. Lid1+ Ura+ transformants were picked and outcrossed to either lid1+ or lid1-6 strains in order to verify cosegregation of the lid1+ phenotype with the ura4+ marker.Isolation of lid1 cDNAs. An S. pombe cDNA library constructed in the vector pDB20 (11) was transformed into Escherichia coli and plated on Luria-Bertani agar containing 50 µg of ampicillin per ml. Approximately 106 transformants were plated. Colonies were allowed to form overnight at 36°C and then lifted onto Hybond-N nylon membranes (Amersham Life Sciences) and processed for radioactive hybridization according to manufacturer's instructions. Membranes were prehybridized in 5× Denhardt's solution-0.5% sodium dodecyl sulfate (SDS)-5× SSPE (1× SSPE is 0.18 M NaCl, 10 mM NaH2PO4, and 1 mM EDTA [pH 7.7])-100 µg of hydrolyzed yeast RNA per ml at 65°C and then hybridized overnight in the same buffer. Two different templates were utilized in order to generate [32P]dCTP-labeled probes: a 1.5-kb lid1+ EcoRI fragment (used to isolate clone pKG1074) and a 0.5-kb 5' lid1+ SacI/XhoI fragment (used to isolate pKG1142). The isolated plasmids were sequenced by using gene-specific oligonucleotide primers.
Deletion of lid1 from the genome.
In order to
generate a lid1 deletion construct containing
lid1+ 5' and 3' flanks, an ~4-kb
lid1+ genomic fragment
(BglII/BstXI) was subcloned from pKG1030 into pBS-SK+ (Stratagene, La Jolla, Calif.) to generate pKG1186.
A portion of the lid1 coding region
(XhoI/EcoRV) was excised from pKG1186 and
replaced with a 1.8-kb fragment containing the
ura4+ gene, to generate pKG1191. A
SacI/Acc651 fragment consisting of
lid1 5'
flank::ura4+::lid1
3' flank was isolated from pKG1191 and transformed into a diploid
strain (h+/h
ura4-D18/ura4-D18
leu1-32/leu1-32 ade6-M210/ade6-M216). Ura+
transformants were selected on medium lacking uracil. Uracil prototrophs were isolated, and genomic DNA was prepared and digested with BglII and HindIII. Digests were
separated by agarose gel electrophoresis, blotted to membranes, and
hybridized with an [
-32P]dCTP-labeled 1-kb
BglII/XhoI fragment of lid11 5' flank,
in order to verify replacement of one allele of lid1 with
the ura4+ cassette in the Ura+
diploids. Diploids were allowed to sporulate, and tetrads were dissected in order to analyze the
lid1::ura4+ phenotype.
Epitope tagging of lid1p.
A genomic version of
lid1 encoding nine copies of the myc epitope fused to the C
terminus of lid1 was generated by the method described previously
(1). In brief, the oligonucleotide primers lid1tag1 (5' CCT GTA TCT AGA TGC CAC TTT GGC-3') and
lid1tag3 (5'-GGG GAT CCG TCG ACC TGC AGC GTA CGA AAA AGA GAA
TAA ACG ATA TCT CG-3') were synthesized in order to PCR amplify a
400-bp lid1 genomic fragment upstream of the putative
lid1 stop codon, and the primers lid1tag2 (5'-TTA
TAT ATA AGG TAC CTT GAT TC-3') and lid1tag4 (GTT TAA ACG AGC
TCG AAT TCA TCG ATA TGA GCT TAT GTT TAA TGG TCG-3') were synthesized in
order to PCR amplify lid1 genomic sequence downstream of the
putative lid1 stop codon, using the thermostable DNA
polymerase Pfu (Stratagene) according to the manufacturer's
instructions in a PTC-100 Programmable Thermal Controller (MJ Research)
programmed as follows: 95°C for 1 min, 56°C for 1 min, and 72°C
for 3 min (40 cycles); 94°C for 1 min; 56°C for 2 min; and 72°C
for 10 min. PCR fragments were agarose gel purified by using the
QIAquick Gel Extraction System (QIAGEN) according to the
manufacturer's instructions. Approximately 100 ng of each fragment was
used in a second PCR, with a mixture containing 1 µM each
lid1tag1 and lid1tag2 and 200 ng of pKG1198
(encoding the 9xMyc-Kan tag; the 9xMyc cassette was a generous gift of
K. Nasmyth, and pKG1198 was constructed by W. H. McDonald) and
utilizing the Taq Plus Precision System (Stratagene) according to the
manufacturer's instructions, in a PTC-100 Programmable Thermal
Controller (MJ Research) programmed as follows: 95°C for 1 min;
95°C for 1 min, 62°C for 1 min (with an increase of 1°C/cycle),
and 72°C for 5 min (15 cycles); 95°C for 1 min, 50°C for 1 min,
and 72°C for 5 min (30 cycles); and 72°C for 10 min. The
amplification product was agarose gel purified and transformed into
diploid cells (h+/h
ura4-D18/ura4-D18
leu1-32/leu1-32 ade6-M210/ade6-M216) by the lithium acetate
method, as described previously (25). Transformants were
plated on YE agar, allowed to recover overnight at 32°C, and then
replica plated to YE agar containing 25 µg of G418 per ml.
G418-resistant (G418r) diploids were picked and allowed to
sporulate. Tetrads were dissected and analyzed for segregation of the
G418r marker. G418r colonies derived from
tetrads which segregated 2 G418r:2 G418s
progeny were picked and further analyzed. Genomic DNA was prepared and
digested with SalI and NdeI. Digests were
separated by agarose gel electrophoresis, blotted to membranes, and
hybridized with an [
-32P]dCTP-labeled 600-bp
HindIII lid1 fragment, in order to verify integration of the lid1 tag at the lid1 genomic
locus in G418r colonies. Protein lysates were prepared as
described previously (16) and subjected to
immunoprecipitation by consecutive incubation with (i) the monoclonal
anti-Myc antibody 9E10 (2 µg/ml), (ii) rabbit anti-mouse
immunoglobulin G (IgG) antibody (Organon Teknika Corp., West Chester,
Pa.), and (iii) protein A-Sepharose (Pharmacia Biotech).
Immunoprecipitates were washed extensively with Nonidet P-40 (NP-40)
buffer. Lysates and immunoprecipitates were resolved on SDS-6 to 20%
polyacrylamide gradient gels and then transferred to Immobilon-P
(Millipore, Bedford, Mass.). For detection of lid1p-myc, the blot was
incubated consecutively with 9E10 (2 µg/ml), peroxidase-conjugated sheep anti-mouse IgG (1:3,000; Sigma Chemical Co., St. Louis, Mo.), and
enhanced chemiluminescence (ECL) detection reagents (Amersham Life
Sciences), followed by chemiluminescence detection with Reflection
NEF-596 autoradiography film (NEN Life Science Products).
Epitope tagging of cut9p. Epitope tagging of Cut9 was performed as described above for epitope tagging of lid1, using the 5' flank oligonucleotide primers cut9tag1 (5'-GAT GCC CTT AAC CAA GGG-3') and cut9tag2 (5'-GGG GAT CCG TCG ACC TGC AGC GTA CGA TCG TTG CTC TGA GAC ATT ACC TTC-3') and the 3' flank oligonucleotide primers cut9tag3 (5'-GTT TAA ACG AGC TCG AAT TCA TCG ATA TTG CGA AAT TCT ATT AAT TCT TG-3') and cut9tag4 (5'-GAA TTC TGC CGC TTC TAT G-3'). The second PCR was performed with pKG1155 (encoding the 3xHA-Kan tag; a generous gift of J. Bahler and J. Pringle) as the template. The purified amplification product was transformed directly into haploid wild-type cells (KGY28). G418r colonies were picked and analyzed. Genomic DNA was prepared and digested with BamHI. Digests were separated by agarose gel electrophoresis, blotted to membranes, and then probed with the cut9 5' flank PCR fragment to verify integration of the 3xHA-Kan construct at the cut9 locus. Protein lysates were prepared as described above and subjected to immunoprecipitation by consecutive incubation with (i) the monoclonal antihemagglutinin (anti-HA) antibody HA.11 (5 µg/ml; Berkeley Antibody Company, Richmond, Calif.) or the monoclonal anti-HA antibody 12CA5 (5 µg/ml), (ii) rabbit anti-mouse IgG antibody (Organon Teknika Corp.), and (iii) protein A-Sepharose (Pharmacia Biotech). Immunoprecipitates were washed extensively with NP-40 buffer. Lysates and immunoprecipitates were resolved on SDS-6 to 20% polyacrylamide gradient gels and then transferred to Immobilon-P (Millipore). For detection of cut9p-HA, the blot was incubated consecutively with HA.11 or 12CA5 (5 µg/ml), peroxidase-conjugated sheep anti-mouse IgG (1:3,000; Sigma Chemical Co.), and ECL detection reagents (Sigma Chemical Co.), followed by chemiluminescence detection with Reflection NEF-596 autoradiography film (NEN Life Science Products). For quantitation of immunoblotting data, ECL Plus reagents (Amersham Life Science) were used. Data were collected on a Molecular Dynamics Storm instrument and quantified by ImageQuant version 1.1.
Epitope tagging of cut2p. Epitope tagging of cut2p was performed as described above for epitope tagging of lid1p, using the 5' flank oligonucleotide primers cut2tag1 (5'-CAC CTG CAT CAG ATT TCC-3') and cut2tag3 (5' GTT TAA ACG AGC TCG AAT TCA TCG ATA AAA GAT TAC GAA TTT TCA GGT TTT GTG-3') and the 3' flank oligonucleotide primers cut2tag2 (5'-GGG GAT CCG TCG ACC TGC AGC GTA CGA TAA CAA TCC TGT ATC CAA AGA TG-3') and cut2tag4 (5'-GAA TGT GTG CAT CTG CTG-3'). The second PCR was performed with pKG1262 (encoding 13 copies of the myc epitope; from J. Bahler and J. Pringle) as the template. The purified amplification product was transformed directly into haploid cells (KGY28). G418r colonies were picked and analyzed for the correct integration event by PCR.
In vivo 35S labeling.
Wild-type cells (KGY28) or
lid1::lid1-myc cells (KGY1302) were
grown to mid-log phase in minimal medium at 32°C. A total of 2 × 108 cells were collected by centrifugation, resuspended
in 10 ml of minimal medium containing 1 mCi of
Tran35S-label (ICN Pharmaceuticals, Inc., Irvine, Calif.),
and then incubated with vigorous shaking at 32°C for 4 h. Cell
lysates were prepared, and immunoprecipitation of lid1p-myc was
performed as described above. Immunoprecipitates were resolved by
SDS-polyacrylamide gel electrophoresis (SDS-PAGE) on 6 to 20% gradient
gels. Gels were treated with Amplify (Amersham Life Sciences), dried on
a vacuum gel dryer, and exposed to X-ray film at
80°C.
Sucrose gradient analysis. For sucrose gradient analysis, cells were grown to mid-log phase in YE medium at 32°C. Approximately 2 × 108 cells were collected by centrifugation, and native lysates in NP-40 buffer were prepared as described above. Lysates were layered on 10 to 30% sucrose gradients prepared in NP-40 buffer. Gradients were ultracentrifuged at 30,000 rpm for 21 h in a Beckman SW50.1 rotor. Sedimentation markers were fractionated on gradients prepared and spun in parallel. Fractions were collected, run on SDS-6 to 20% polyacrylamide gradient gels, and then immunoblotted as described above.
Coimmunoprecipitation analysis of lid1p-myc and cut9p-HA. Native lysates were prepared from KGY1302 (lid1::lid1-myc), KGY1365 (cut9::cut9-HA), or KGY1366 (lid1::lid1-myc cut9::cut9-HA) cells as described above. Denatured lysates were prepared as for native lysates, except that lysed cells were heated to 100°C for 2 min in 300 µl of SDS lysis buffer (10 mM NaPO4 [pH 7.0], 1% SDS, 1 mM dithiothreitol, 1 mM EDTA, 50 mM NaF, 100 µM Na3VO4, 4 µg of leupeptin per ml) prior to extraction with NP-40 buffer. Immunoprecipitations were performed with 9E10 or HA.11 as described above. Immunoprecipitates were resolved by SDS-PAGE, blotted to polyvinylidene difluoride (PVDF) membranes, and probed for lid1p-myc or cut9p-HA as described above.
Ubiquitination assay. To assay APC/C activity towards cut2p-myc, we followed procedures outlined by Benito et al. (4). The relevant strains were transformed with pREP1-His6-ubiquitin plasmid (a gift from Sergio Moreno). Following growth in the absence of thiamine for 22 h, cells were shifted to the nonpermissive temperature for 4 h and protein lysates were prepared as described previously (4). Briefly, cells were lysed in 8 M urea-100 mM sodium phosphate (pH 8.0)-5 mM imidazole. Cell extracts were clarified by centrifugation for 5 min, and the protein concentration in the supernatants was determined. Six milligrams of extract was mixed with Ni2+-nitrilotriacetic acid (Ni2+-NTA) agarose (Qiagen) and incubated for 4 h at room temperature. The resin was washed exactly as described previously (4). The eluate was diluted in 5× sample buffer and boiled for 5 min, and ubiquitinated forms of cut2p-myc were detected by immunoblotting with 9E10 antibody as described above.
Analysis of protein levels through the cell cycle. A synchronized population of KGY1366 cells was isolated by centrifugal elutriation and then inoculated into fresh medium at 32°C. Approximately equivalent numbers of cells were collected at 20-min intervals for preparation of whole-cell lysates as described above. Lysates were resolved by SDS-PAGE and immunoblotted for cut9p-HA, lid1p-myc, and cdc13p, as described above, and for arp3p as a loading control. Antibodies to arp3p (31) were utilized at a dilution of 1:5,000, and affinity-purified rabbit anti-Cdc13 antibodies (GJG56) were used at a dilution of 1:500. Detection was as described above for lid1p-myc, except that peroxidase-conjugated sheep anti-rabbit IgG (1:10,000; Sigma Chemical Co.) was used as the secondary antibody. cdc2p was detected on immunoblots by incubation with anti-PSTAIRE monoclonal antibody (1:1,000; Sigma Chemical Co.), further incubation with peroxidase-conjugated goat anti-mouse IgG (1:50,000; Jackson ImmunoResearch laboratories, Inc.), and then ECL.
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RESULTS |
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Isolation of dim1-interacting genes: the lid screen. As described previously, the dim1 gene was isolated and shown to encode an evolutionarily conserved protein essential for mitosis (5). In order to investigate further the nature of dim1 function, we wished to identify other proteins with which dim1p interacts in S. pombe cells. We took a genetic approach to this problem, choosing to isolate and characterize second-site mutations synthetically lethal with dim1-35. To accomplish this, a dim1-35 strain carrying pREP1-mdim1 was mutagenized and plated on medium lacking thiamine in order to induce expression of mdim1. Colonies were then replica plated to medium containing thiamine in order to eliminate mdim1 activity. Under these conditions, we expected dim1-35 lid (for lethal in dim1-35) double mutants to be inviable. A total of 85,000 mutagenized colonies were screened; 88 were picked based on inviability in the presence of thiamine. Of these, 26 were outcrossed. Upon outcrossing, four of the mutant strains could not be analyzed due to poor spore viability. Based upon linkage between dim1-35 and the lid mutation in each case, 10 of the remaining 22 strains appeared to contain unconditional loss-of-function alleles of dim1, while 12 contained second-site lid mutations unlinked to the dim1 locus. Of the lid mutants, only the lid1-6 mutant demonstrated a temperature-sensitive phenotype when outcrossed from the dim1-35 mutant. Therefore, we chose to focus our efforts on the analysis of lid1.
dim1-interacting gene lid1. lid1-6 did not display strict synthetic lethality in a dim1-35 background. When the outcrossed lid1-6 mutant was crossed against the dim1-35 mutant, viable lid1-6 dim1-35 double mutants were recovered. The double-mutant cells, however, did display a near-lethal phenotype at either 25 or 29°C, temperatures fully permissive for either lid1-6 or dim1-35 single mutants (Fig. 1A). The double mutant grew extremely slowly and exhibited numerous cytological defects, including cutting and segregation of DNA to only one daughter cell (Fig. 1B, panel a), whereas either lid1-6 or dim1-35 single mutants were phenotypically wild type at these temperatures (Fig. 1B, panels b and c).
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Cloning and sequencing of lid1. In order to analyze lid1 at a molecular genetic level, the lid1 gene was cloned by complementation of the lid1-6 temperature-sensitive phenotype. After transformation of the lid1-6 mutant with an S. pombe genomic library, two rescuing plasmids, each containing a 5.5-kb insert, were isolated (pKG1030). The isolated plasmids were shown to be identical by restriction mapping and Southern blot analyses. Integration mapping confirmed that the isolated gene contained the lid1 gene and not a high-copy suppressor. Sequencing revealed that a portion of the insert was contained within c19g12, a cosmid located on the short arm of chromosome I (21), which was sequenced as part of the S. pombe genome sequencing project. Sequencing of the remainder of the insert, in combination with the c19g12 sequence, revealed a single large open reading frame (ORF). The minimal rescuing fragment, however, extended beyond this ORF, suggesting that the gene included several smaller upstream ORFs, separated by introns (Fig. 2A). Therefore, a cDNA library was screened in order to isolate a lid1 cDNA. Two independent clones, one a partial cDNA at the 3' end of the gene, containing the putative stop codon, and one a partial cDNA at the 5' end of the gene, were isolated. The 5' clone revealed the existence of four introns. Analysis of the genomic clone revealed an in-frame start codon 124 bp upstream of the first intron. Together, then, the isolated clones comprised an ORF (Fig. 2A) encoding a predicted protein product of 719 amino acids and 82.5 kDa (Fig. 2B). Comparison of the predicted amino acid sequence of lid1p with protein sequences available in the databases revealed no significant homologies or motifs (but see Discussion).
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Deletion of lid1 from the S. pombe
genome.
In order to determine whether lid1 is an
essential gene in S. pombe, the method of one-step gene
disruption was used in order to replace a 3-kb fragment of DNA within
the lid1 minimal rescuing fragment with the
ura4+ selectable marker in diploid S. pombe cells (see Materials and Methods) (Fig. 2A). Replacement of
one allele of lid1 with the ura4+
cassette in Ura+ diploids was confirmed by Southern blot
analysis (data not shown). Ura+ diploids were allowed to
sporulate, and tetrads were dissected. Thirty-five tetrads segregated 2 inviable:2 viable Ura
progeny. The inviable progeny
underwent spore germination, and then two or three residual cell
divisions, before arresting as microcolonies of six to eight cells
(data not shown). Therefore, lid1 encodes an essential gene
in S. pombe.
lid1p-myc associates with several other proteins in vivo. In order to investigate lid1 function at a biochemical level, a DNA fragment encoding nine copies of the myc epitope tag was integrated at the lid1 genomic locus, just upstream of the putative lid1 stop codon (Fig. 2) (see Materials and Methods). The anti-myc monoclonal antibody 9E10 detected a protein which migrated with an apparent molecular mass of ~100 kDa in lysates and 9E10 immunoprecipitates prepared from the epitope-tagged strain (lid1::lid1-myc; KGY1302) (Fig. 3A). This molecular mass corresponded to that predicted from the addition of the multiple myc epitope tags to the endogenous 82.5-kDa protein. This protein was not detected when lysates or 9E10 immunoprecipitates from wild-type cells were probed with the 9E10 antibody (data not shown).
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lid1-myc cosediments with cut9-HA. The specific, in vivo association of lid1p-myc with proteins of ~160, ~75, and ~65 kDa (Fig. 3B) was consistent with the hypothesis that lid1p may comprise a component of the APC/C in S. pombe. (APC/C components cut4p, cut9p, and nuc2p are proteins of 166, 78, and 67 kDa, respectively [18, 40, 49]). In order to examine further the possibility that lid1 may encode an APC/C component, an epitope-tagged version of the APC/C component cut9p was generated by integrating a DNA fragment encoding three copies of the HA epitope into the S. pombe genome just upstream of the cut9 stop codon (see Materials and Methods). Lysates from the epitope-tagged strain (cut9::cut9-HA; KGY1365) were subjected to immunoprecipitation and immunoblot analysis with the monoclonal anti-HA antibody HA.11. A protein which migrated with an apparent molecular mass of ~90 kDa was detected in KGY1365 lysates and HA.11 immunoprecipitates (Fig. 3C) but not in wild-type lysates or immunoprecipitates (data not shown).
In order to determine whether lid1p cosediments with the APC/C, the sedimentation profiles of lid1p-myc and cut9p-HA were compared. A lysate from a double-tagged strain (lid1::lid1-myc cut9::cut9-HA) was prepared and subjected to sucrose gradient sedimentation analysis. Gradient fractions were collected, resolved by SDS-PAGE, blotted to membranes, and probed with either the anti-HA monoclonal antibody 12CA5 to detect cut9p-HA or the anti-myc monoclonal antibody 9E10 to detect lid1p-myc. lid1p-myc peaked three times: once in fraction 6, again in fraction 10, and lastly in fraction 15, which would correspond to monomeric lid1p-myc (Fig. 4A, panel a). cut9p-HA showed a bimodal distribution (Fig. 4A, panel b), as shown previously for the endogenous cut9 protein (47, 49). Significantly, the high-molecular-weight subpopulation of cut9p-HA peaked in fraction 6, along with lid1p-myc, at just greater than 19S. This high-molecular-weight fraction of cut9p-HA contained more slowly migrating forms of cut9p-HA which have been shown previously to be the result of phosphorylation (47).
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lid1p-myc associates with cut9p-HA and nuc2p in vivo. The cosedimentation of lid1p-myc and cut9p-HA in sucrose gradients, as well as the failure of lid1p-myc to migrate in a high-molecular-weight complex in a cut9-665 background, further suggested a physical interaction among lid1p and cut9p and/or other APC/C components. In order to determine directly whether lid1p-myc and cut9p-HA associate in vivo, native or denatured lysates were prepared from KGY1302 (lid1::lid1-myc), KGY1365 (cut9::cut9-HA), or KGY1366 (lid1::lid1-myc cut9::cut9-HA) cells. Lysates then were subjected to immunoprecipitation and immunoblot analysis with 9E10 or HA.11 antibodies. Probing with 9E10 revealed a band of ~100 kDa (lid1p-myc) in KGY1302 and KGY1366 native lysates, as well as in KGY1302 denatured lysates, but not in KGY1366 denatured lysates or KGY1365 native or denatured lysates. Conversely, probing with HA.11 revealed a band of ~90 kDa (cut9p-HA) in KGY1365 and KGY1366 native cell lysates, as well as in KGY1365 denatured cell lysates, but not in KGY1366 denatured lysates or KGY1302 native or denatured lysates (Fig. 4B). Less lid1p-myc was immunoprecipitated with HA antibodies than with 9E10 antibodies, presumably because not all lid1p is within the 20S complex (compare Fig. 4A, panels a and b). Coimmunoprecipitation of lid1p-myc with known components of the S. pombe APC/C was confirmed by using polyclonal antibodies against nuc2p and cut9p (a generous gift of M. Yanagida) (Fig. 4C).
lid1p is required for the multiubiquitination of cut2p. To test directly whether lid1p was required for the E3 ligase activity of the APC/C, we examined the ubiquitination of cut2p, a known destruction box-containing APC/C target (12, 17), in the presence and absence of lid1p function. cut2p is required for sister chromatid separation and is targeted for APC/C-mediated destruction at the onset of anaphase (12). In order to detect cut2p readily, we placed sequences encoding 13 copies of the myc epitope tag at the 3' end of the cut2 coding region; the tagged version was fully functional in that the cut2::cut2-myc strain was indistinguishable from the wild type in morphology and growth rate. A doublet at ~62 kDa corresponding to cut2p-myc was readily detected by immunoblotting with 9E10 (Fig. 5A); endogenous cut2p is 42 kDa and also migrates as a doublet in SDS-PAGE (12). The cut2::cut2-myc allele was crossed into an mts3-1 strain with or without the lid1-6 mutation. mts3+ encodes subunit 14 of the 26S proteasome (15), and in the mts3-1 mutant strain, multiubiquitinated conjugates accumulate at the nonpermissive temperature because of their failure to become degraded (4, 15). Thus, cut2p-myc would be expected to accumulate ubiquitin conjugates in the mts3-1 mutant but only if the APC/C was active. To allow us to purify ubiquitin-conjugated proteins, a His6-tagged version of ubiquitin was expressed in wild-type, mts3-1, mts3-1 cut2::cut2-myc, and mts3-1 cut2::cut2-myc lid1-6 strains. Extracts from these strains were purified by using Ni2+-NTA resin and separated by SDS-PAGE, and ubiquitinated cut2p-myc was detected by immunoblotting. High-molecular-weight bands were detected in the mts3-1 cut2::cut2-myc strain expressing His6-ubiquitin at the restrictive temperature (Fig. 5, lanes 4). These bands were much reduced in the mts3-1 cut2::cut2-myc lid1-6 strain (Fig. 5, lanes 3). They were absent from the wild-type and mts3-1, strains which do not express myc epitope-tagged proteins (Fig. 5, lanes 1 and 2). This result clearly establishes that lid1p is required for APC/C-mediated ubiquitination of cut2p.
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dim1+ function is required to maintain lid1p levels. To investigate the basis for the negative genetic interaction between lid1-6 and dim1-35, we examined whether an epitope-tagged version of dim1p, dim1p-HA, could be coimmunoprecipitated with lid1p-myc. We found no evidence for such a stable association (data not shown). We also examined the level of lid1p-myc in the dim1-35 mutant. Interestingly, we found that it was reduced significantly (three- to fourfold in separate experiments as quantified with the use of a Molecular Dynamics Storm instrument) compared with that in wild-type cells grown at 36°C (Fig. 6A). In contrast, the level of cut9p-HA was not affected significantly in dim1-35 cells (Fig. 6A and data not shown). To examine the effect of dim1+ loss on lid1p-myc levels in a different manner and at a different arrest point within the cell cycle, we crossed the lid1::lid1-myc cassette into strain KGY1180, which contains a dim1 null allele and a conditional expression cassette of the dim1+ cDNA. More specifically, KGY1180 contains a single integrated version of dim1+ cDNA under control of the thiamine-repressible nmt1-T81 promoter. When grown in medium lacking thiamine, this strain is phenotypically wild type, but when placed in medium containing thiamine, the cell number stops increasing by 13 h and cells arrest in G2 phase due to the loss of the essential dim1p (5). Protein lysates were prepared from samples of this strain collected periodically after a shift to thiamine-containing medium, and the level of lid1p-myc was determined by immunoblotting equal amounts of protein. As shown in Fig. 6B, lid1p-myc levels began to drop at 6 h and fell to very low levels by 10 h (before complete cell cycle arrest), whereas the level of the loading control, arp3p, did not change. In a second experiment examining the consequence of the loss of dim1+ function for the abundance of lid1p-myc, we compared the level of lid1p-myc with that of cdc2p (Fig. 6C). Again, lid1p-myc levels were significantly reduced by 10 h after shutoff of nmt1-T81 dim1+, whereas the level of cdc2p did not change. Thus, the abundance of lid1p-myc depends upon the function of dim1+.
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dim1+ function is required for the multiubiquitination of cut2p. Given that the abundance of the 20S APC/C complex declined in the absence of dim1+ function, we reasoned that the activity of the APC/C might also be compromised. To test this possibility, we constructed a dim1-35 mts3-1 cut2::cut2-myc strain and introduced the His6-tagged version of ubiquitin into it. When this strain was tested for the ubiquitination of cut2p-myc following a shift to the nonpermissive temperature, in parallel with the strains described above, we found that cut2p-myc ubiquitination was abolished in the absence of dim1+ function (Fig. 5C, lane 6). The immunoblot in Fig. 5D shows that cut2p-myc was present in the dim1-35 and lid1-6 protein lysates from which the ubiquitin-conjugated proteins were purified. Taken together, these data indicate that dim1+ function is required for APC/C function.
lid1p-myc protein levels are constant through the cell cycle. Because of the decrease in lid1p levels in the absence of dim1 function in both dim1-35 cells, which arrest in mitosis, and dim1 null cells, which arrest at the G2/M transition, we became interested to determine whether lid1p-myc levels varied through the cell cycle. To this end, a synchronized G2 population of lid1::lid1-myc cut9::cut9-HA (KGY1366) cells was isolated by centrifugal elutriation. Samples were collected as cells progressed through two synchronous cell cycles. The levels of cut9p-HA and cdc13p (as positive controls for cell cycle periodicity), arp3p (as a loading control), and lid1p-myc were determined by immunoblotting. The hyperphosphorylated form of cut9p-HA was observed just prior to each peak of septation (Fig. 8a, t = 40 min and t = 180 min), as was reported previously (47). cdc13p levels are known to fall during mitosis (7, 13), and indeed we observed that cdc13p levels dropped coincident with each septation peak (Fig. 8b, t = 60 min and t = 200 min). In contrast, lid1p-myc levels did not undergo any significant changes through the cell cycle, nor did lid1p-myc undergo any detectable shifts in electrophoretic mobility suggestive of posttranslational modifications (Fig. 8c). We also examined lid1p-myc levels in a cdc25-22 block-and-release experiment, which provides a higher degree of cell cycle synchrony. Again, we did not observe any fluctuation in lid1p-myc levels (data not shown).
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| |
DISCUSSION |
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Identification of lid1p, a component of the S. pombe APC/C. dim1p is a 17-kDa, evolutionarily conserved, essential protein. A temperature-sensitive allele of dim1, dim1-35, causes arrest in mitosis and inability to initiate chromosome segregation, although spindle elongation occurs. In contrast, cells containing a null mutation in dim1 are unable to enter mitosis and block at the G2/M transition (5). To gain further insight into dim1p function, we performed a synthetic lethal screen aimed at identifying proteins that interact with dim1p. Here, we report our characterization of one lid (for lethal in dim1-35) mutant, the lid1-6 mutant. In a dim1+ background, lid1-6 causes a temperature-sensitive phenotype. Specifically, lid1-6 mutant cells are unable to undergo anaphase at the restrictive temperature; short metaphase spindles form but do not elongate, and the chromosomes do not separate. Based on this phenotype, which is similar to that of cut4 and cut9 mutants (40, 49), we hypothesized that lid1+ might encode a component of the S. pombe APC/C, since cut4p and cut9p are established APC/C components (47, 49). The APC/C is a 20S complex that acts as an E3 ubiquitin ligase essential for anaphase onset in all eukaryotes examined (reviewed in references 8, 17, 26, and 44).
In order to test the hypothesis that lid1 may encode an APC/C component, we cloned the lid1 gene by complementation of the lid1-6 temperature-sensitive phenotype. DNA sequencing and hypothetical translation of the lid1 gene provided no clues as to the function of lid1. However, consistent with the notion that lid1+ encodes a component of the APC/C, an epitope-tagged variant of lid1p, lid1p-myc, coimmunoprecipitated with several other proteins, including cut9p and nuc2p, which are known members of the S. pombe APC/C. The results of sucrose gradient analysis also are consistent with the interpretation that lid1p is a component of the S. pombe APC/C; lid1p-myc cosediments with cut9p-HA at ~20S, the sedimentation profile of lid1p-myc depends upon functional cut9+, and the ability of cut9p-HA to sediment at 20S depends upon functional lid1+. Furthermore, lid1p function is required for the multiubiquitination of cut2p, a known target of the APC/C (12, 13). These data establish that lid1p is a component of the S. pombe APC/C and also that its function is necessary for maintaining the integrity of the 20S APC/C. Our comparison of the predicted lid1 protein sequence with sequences available in the databases revealed no significant homologies or motifs. Our failure to detect a budding yeast homolog was especially surprising given our assumption that the APC/C components would be conserved between budding and fission yeasts. However, while this work was in progress, the sequences of most, if not all, components of the human and yeast APC/Cs were reported (50, 52). When the sequence of the human APC4 protein was used as a query to probe databases, limited similarity between it and S. pombe ORF Z97209 was observed, but no homolog was detected in budding yeast (50). S. pombe ORF Z97209 encodes lid1p. Budding yeast Apc4p also was reported to have weak similarity with S. pombe ORF Z97209 (52). We have aligned lid1p with APC4 and Apc4p and have found a central region of 133 or 134 amino acids which contains significant sequence conservation (Fig. 9). There is 24% identity and 34% similarity between S. pombe lid1p and human APC4 in this region and 22% identity and 31% similarity between S. pombe lid1p and S. cerevisiae Apc4p. Outside this region, there is little sequence similarity among the three proteins, although there are two other stretches of sequence similarity between S. pombe lid1p and human APC4 (data not shown). Taken together, these protein sequence comparisons indicate that lid1p, APC4, and Apc4p are distantly related, and it will be interesting to determine whether they are conserved functionally (50). The isolation of a conditional lethal mutation in the S. pombe component most similar to both human APC4 and budding yeast Apc4p provides an excellent opportunity to test this directly; the lack of sequence conservation makes it unlikely that cross complementation of the yeast null alleles would be successful.
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dim1p is required for APC/C integrity and activity. The APC/C is active towards destruction box-containing substrates only during mitosis and G1 phase (reviewed in references 8, 17, 26, and 44). Its activation towards mitotic cyclins in vitro has been attributed to phosphorylation of its components rather than to alterations in its composition or abundance (reviewed in references 8, 17, 26, and 44). For these reasons, we were surprised to learn that the abundance of lid1p fell in the absence of dim1+ function. However, this observation provides a reasonable explanation for the synthetic lethal interaction between lid1-6 and dim1-35. In a dim1-35 mutant background, there is probably an insufficient amount of functional lid1-6p to support cell cycle progression. The loss of lid1p in the absence of dim1 activity is not due to a specific cell cycle block, because lid1p was lost both in dim1-35 and in dim1 null cells. dim1-35 cells arrest in mitosis with a cut-like phenotype, but dim1 null cells arrest at the G2/M transition (5). In terms of understanding the biochemical mechanism of dim1p action, we can now direct our efforts to understanding the role of dim1p in maintaining the level of lid1p. dim1p is not stably associated with lid1p (our unpublished observations), and it will be very instructive to learn whether dim1p affects the stability or synthesis of lid1p or lid1 mRNA. The interaction with lid1p is probably insufficient to explain the essential role of dim1p, however, since overexpression of lid1+ does not rescue the dim1-35 mutant (data not shown).
By determining the sedimentation behavior of cut9p-HA in dim1-35 cells, we have found that the reduction of lid1p in dim1 mutants is translated into a lower level of the 20S APC/C complex. This is not surprising given the interdependence of various components for the integrity of the complex. As two examples, in a cut9 mutant, neither nuc2p nor lid1p remains in a 20S complex; in a nuc2 or lid1 mutant, cut9p does not sediment at 20S (reference 47 and this study). Thus, the failure of dim1-35 cells to execute chromosome segregation can be most easily explained by a reduction of APC/C activity caused by reduced levels of lid1p and the consequent reduction in the amount of the APC/C complex. Consistent with this interpretation, we have shown that loss of dim1+ function abrogates the multiubiquitination of cut2p-myc. Whether the failure of cells carrying the dim1 null allele to enter mitosis can be attributed to the lack of APC/C activity remains to be determined. In addition to the reduced levels of the 20S complex in the dim1-35 mutant, we noted a reduction in the phosphorylation of cut9p-HA. Whether this is a consequence or a cause of the reduction in 20S complex abundance or an unrelated phenomenon also remains to be determined. In summary, we have uncovered a dependency between dim1+ function and the function of the APC/C. Future efforts will be directed at understanding how dim1p affects lid1p abundance and whether it acts through intermediate components to do so.| |
ACKNOWLEDGMENTS |
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We thank J. Bahler, J. Pringle, and K. Nasmyth for providing the epitope tagging cassettes, K. Gull for the TAT-1 monoclonal antibody, S. Moreno for tagged ubiquitin construct and advice on its use, and M. Yanagida for polyclonal antibodies to cut9p and nuc2p. We are grateful to Hayes McDonald for advice on epitope tagging, Ryoma Ohi and Jennifer Morrell for constructive comments on the manuscript, and all members of the Gould lab for their support and advice during the course of this work.
This work was supported by NIH grant 47728 to K.L.G. L.D.B. was supported by a National Science Foundation Graduate Research Fellowship. K.L.G. is an associate investigator of the Howard Hughes Medical Institute.
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FOOTNOTES |
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* Corresponding author. Mailing address: HHMI and Dept. of Cell Biology, Vanderbilt University School of Medicine, Nashville, TN 37232. Phone: (615) 343-9502. Fax: (615) 343-0723. E-mail: kathy.gould{at}mcmail.vanderbilt.edu.
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