Department of Biochemistry and Molecular
Biology, University of New Hampshire, Durham, New Hampshire
03824,1 and Département Biochimie
Médicale, Centre Médical Universitaire de Genève,
1211 Geneva 4, Switzerland2
Received 2 November 1998/Returned for modification 10 January
1999/Accepted 14 June 1999
The CCR4-NOT complex (1 mDa in size), consisting of the proteins
CCR4, CAF1, and NOT1 to NOT5, regulates gene expression both positively
and negatively and is distinct from other large transcriptional complexes in Saccharomyces cerevisiae such as SNF/SWI,
TFIID, SAGA, and RNA polymerase II holoenzyme. The physical and genetic interactions between the components of the CCR4-NOT complex were investigated in order to gain insight into how this complex affects the
expression of diverse genes and processes. The CAF1 protein was found
to be absolutely required for CCR4 association with the NOT proteins,
and CCR4 and CAF1, in turn, physically interacted with NOT1 through its
central amino acid region from positions 667 to 1152. The NOT3, NOT4,
and NOT5 proteins had no significant effect on the association of CCR4,
CAF1, and NOT1 with each other. In contrast, the NOT2, NOT4, and NOT5
interacted with the C-terminal region (residues 1490 to 2108) of NOT1
in which NOT2 and NOT5 physically associated in the absence of CAF1,
NOT3, and NOT4. These and other data indicate that the physical
ordering of these proteins in the complex is CCR4-CAF1-NOT1-(NOT2,
NOT5), with NOT4 and NOT3 more peripheral to NOT2 and NOT5. The
physical separation of CCR4 and CAF1 from other components of the
CCR4-NOT complex correlated with genetic analysis indicating partially
separate functions for these two groups of proteins. ccr4
or caf1 deletion suppressed the increased 3-aminotriazole
resistance phenotype conferred by not mutations, resulted
in opposite effects on gene expression as compared to several
not mutations, and resulted in a number of synthetic
phenotypes in combination with not mutations. These results
define the CCR4-NOT complex as consisting of at least two physically
and functionally separated groups of proteins.
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INTRODUCTION |
The CCR4-NOT complex from
Saccharomyces cerevisiae displays both positive and negative
roles in the regulation of diverse genes and processes (6, 9, 20,
25). This complex, distinct from other large transcriptionally
important complexes such as SNF/SWI, SAGA, SRB-containing polymerase II
holoenzyme, and TFIID (10, 13, 20), consists of two forms, a
1.9 × 106-Da (1.9-mDa) and 1-mDa complex
(20). The smaller complex consists of CCR4, CAF1 (POP2)
(24), the five NOT proteins, and several unidentified
proteins (20, 22, 23). Defects in components of this complex
reduce expression of ADH2 and other nonfermentative genes,
affect the expression of genes involved in cell wall integrity, and
suppress spt10-induced expression at the ADH2
locus (9, 11, 13, 20, 22). Furthermore, mutations in
CCR4 or CAF1 affect cell cycle progression in
late mitosis (22). The NOT genes, in turn, were
originally identified as repressing HIS3 expression from a
noncanonical TATA (TATA-less) element (5, 6), as well as
affecting a number of other genes and processes (1, 8, 16).
The recent demonstration that not and caf1 mutations can suppress a defect in SRB4, a key component of the RNA
polymerase II holoenzyme required for the transcription of most genes
in yeast (19), further indicates a very general repressor role for the CCR4-NOT complex. It has been proposed that the NOT proteins inhibit transcriptional initiation by affecting TATA binding
protein access to TATA-less sequences (4), a model in
agreement with the fact that NOT1 has been found to associate with TATA
binding protein (TBP) (19).
Of the proteins of the CCR4-NOT complex, only NOT1 is an essential
protein (5). The C-terminal residues 1319 to 2108 of NOT1
are sufficient, however, for cells to remain viable (26). Pairwise combinations of not mutations do not in general
lead to synthetic lethality (except for not4 with
not5), suggesting that they form a complex displaying
overlapping functions (6, 23). However, CCR4 and CAF1 appear
in certain contexts to be distinct from the other NOT proteins.
Mutations in the five NOT genes result in increased
resistance to 3-aminotriazole (3-AT) in a partially defective GCN4
background (6). This phenotype is not associated with CCR4
or CAF1 defects (20). Moreover, not mutations
tend to increase HO-lacZ and FKS1-lacZ
expression, whereas a ccr4 or caf1 deletion
reduces expression or has little effect on these promoters
(20). The CCR4 and CAF1 proteins also appear to be strongly
associated; partial disruption of CAF1 inhibits the
association of CCR4 with the NOT1 and NOT2 proteins (20). Therefore, while not alleles have several phenotypes in
common with ccr4 and caf1 defects
(20), notably caffeine, temperature, and magnesium
sensitivities, effects on ADH2 and CYC1 gene
expression, and suppression of spt10-enhanced expression,
CCR4 and CAF1 proteins may functionally and physically represent a
separate group of proteins within the CCR4-NOT complex.
We have analyzed the association of CCR4, CAF1, and the NOT proteins
and related these associations to the phenotypes of the constituents of
this complex. The central segment of NOT1 (residues 667 to 1152) binds
CCR4 and CAF1, whereas the C-terminus of NOT1 (1490 to 2108) associates
with NOT2, -4, and -5. We provide evidence that the arrangement
of the proteins in the complex is CCR4-CAF1-NOT1-(NOT2, NOT5), with NOT3 and NOT4 peripheral to NOT2 and NOT5. Further, the
physical separation of CCR4 and CAF1 from the other NOT proteins correlates, in general, with phenotypes associated with defects in CCR4
and CAF1 compared to the other NOT mutations. The CCR4-NOT complex appears, therefore, to be composed of at least two physically separate groups of proteins that can function differently depending on
the promoter context.
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MATERIALS AND METHODS |
Yeast strains, growth conditions, and enzyme assays.
Yeast
strains (Table 1) were grown at 30°C on
YEP medium (2% yeast extract, 1% Bacto Peptone) or selective medium
(7) supplemented with 5% glucose or with 2% galactose and
2% raffinose unless otherwise indicated. 
-Galactosidase assays and
alcohol dehydrogenase (ADH) assays were carried out as described
previously (12). Assay values represent the averages of at
least three independent assays. The yeast transformation protocol was
as described previously (7, 17).
DNA constructions.
The LexA-NOT1 plasmids containing various
length of NOT1 were constructed as follows. For expression
of LexA-NOT1(667-1152), pLexA-NOT1 was cut with BamHI and
XhoI and the segment carrying codons 667 to 1152 was ligated
with pLexA202-4 (7) cut with the same two enzymes. For
expression of LexA-NOT1(1480-2108), pET28a-NOT1
(XbaI-SalI) was cut with BamHI and
SalI and the segment carrying codons 1480 to 2108 was
inserted into the BamHI and SalI sites of
pLexA-202-2. For expression of LexA-NOT1(1-667), pLexA-NOT1 was cut
with BamHI and SalI, the ends were filled in with
the large subunit of Escherichia coli DNA polymerase
(Klenow), and the plasmid was religated. For expression of
LexA-NOT1(1-1152), pLexA-NOT1 was cut with EcoRI and
XhoI and the fragment encoding residues 1 to 1152 of NOT1
was ligated with pLexA202-2 cut with EcoRI and
SalI. For expression of LexA-NOT1(667-2108), pLexA-NOT1 was
cut with BamHI and SalI and the piece encoding
residues 667 to 2108 was inserted into the BamHI and
SalI sites of pLexA202-2. Expression of all fusion proteins
was confirmed by Western blot analysis.
Antibodies and immunoprecipitation.
For Western analysis,
the antibodies were directed against glutathione
S-transferase (GST)-CAF1, GST-NOT2, His6-NOT5,
GST-NOT1(1480-2108), and GST-DHH1(267-506) fusion proteins. Western
analysis was conducted as described previously (13).
Immunoprecipitations were carried out as previously described
(12). The CAF1 antibody was partially purified as described
elsewhere (14).
Gel filtration chromatography.
The procedure for gel
filtration chromatography using a Superose 6 10/30 column was performed
as described in detail elsewhere (20) except that the
running buffer consisted of 50 mM Tris, 150 mM potassium acetate, and
0.02% Tween 20 only. The flow rate was 0.2 ml/min, and 0.5 ml was
collected per fraction. Molecular weights for each fraction were
calculated based on the elution volumes of blue dextran (7.5 ml),
thyroglobin (12 ml), and bovine serum albumin (16 ml).
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RESULTS |
CAF1 is required for CCR4 association with the NOT proteins.
We had shown previously that deleting CAF1 removed CCR4
completely from the 1-mDa CCR4-NOT complex and reduced significantly but did not eliminate CCR4 association in the 1.9-mDa complex (20). We have also shown that CCR4 is dependent on CAF1 in
its association with NOT1 and NOT2 (20). Using a complete
deletion of CAF1, we further investigated the dependency on
CAF1 for CCR4 for interaction with the other NOT proteins. In a
wild-type strain, immunoprecipitation of CCR4 with anti-CCR4 antibody
brought down NOT1 through NOT5 (Fig. 1,
lane 3). In contrast, in a caf1 deletion strain, none of the
NOT proteins coimmunoprecipitated with CCR4 (lane 4), although all NOT
proteins were present in the crude extract (lane 2). CAF1 protein is
therefore required for CCR4 to associate with all NOT proteins.
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FIG. 1.
CCR4 requires CAF1 to immunoprecipitate NOT proteins.
Immunoprecipitations with CCR4 antibody were conducted in
caf1 (A792, pop2) and wild-type (A790) strains.
Lanes 1 and 2, protein extracts from strains A790 and A792,
respectively; lanes 3 and 4, immunoprecipitated (Ip) proteins analyzed
by Western analysis using antibodies directed against NOT1 through NOT5
and CCR4. The NOT1 antibody used in these experiments could not detect
NOT1 protein in crude (cr.) extracts (lanes 1 and 2), but other results
indicate that NOT1 is present in both CAF1- and
caf1-containing strains (20).
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Physical interactions of CCR4-CAF1-NOT1 are independent of the
NOT3, NOT4, and NOT5 proteins.
Since the above results suggest
that the arrangement of proteins is CCR4-CAF1-NOTs, we subsequently
examined what factors were required for CCR4, CAF1, and NOT1 to
associate. Immunoprecipitation of CCR4 showed that NOT1 and CAF1 can be
coimmunoprecipitated in not3-, not4-, or
not5-deleted backgrounds (Fig.
2A, lanes 3 to 5). (For lane 5, the CAF1
protein was clearly visible in the original Western results.) The same
results were obtained when anti-CAF1 antibody was used for
immunoprecipitation (data not shown). The observation that the
CCR4-CAF1 interaction was not dependent on NOT5 was further confirmed
by gel filtration analysis (Fig. 2B, middle panel). In a
not5 strain, CCR4 and CAF1 cofractionated in both 1.9-mDa
(fractions 3 and 4) and 0.8-mDa (fractions 11 to 13) complexes which
have been previously described for CCR4 and CAF1 (20) (Fig.
2B, top panel, in which CCR4 migrates in fractions 3 and 4 and
fractions 10 to 12). It should be noted that the smaller complex in the
not5 strain runs at a slightly smaller size (0.8 mDa) than
the wild-type strain (0.9 mDa), probably due to loss of the NOT5 and
other potential proteins. Also, the 0.9-mDa CCR4-NOT complex observed
for the wild-type strain runs at slightly smaller size than in the
strains used in our previous study (20).
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FIG. 2.
CCR4 associates with CAF1 in the absence of
NOT3, NOT4, NOT5, and the N-terminal
396 residues of NOT1. (A) Immunoprecipitations (Ip) were conducted with
anti-CCR4 antibody. Western analysis was conducted with antibody
directed against NOT1, NOT3, CCR4, NOT4, CAF1, NOT2, or NOT5 as
indicated. An enhanced chemiluminescence-based system was used for
NOT1, CCR4, and NOT5 Western blots for lanes 1 to 4, whereas an
alkaline phosphatase-based system was used for the remainder of the
results. Strains: wild type (wt), KY803; not1-2, MY8;
not3, MY508; not4, MY537; not5,
MY1735. (B) Yeast extracts from KY803 (wild type [wt]), 1393-4a
(not2), and MY1735 (not5) were analyzed by gel
filtration chromatography using a Superose 6 10/30 column. The protein
extracts were precleared by centrifugation at 100,000 × g for 1 min, and 200 µl of sample was loaded onto the column.
The flow rate was 0.2 ml/min, and a 0.5-ml volume was collected in each
fraction; 100 µl from each fraction were analyzed by sodium dodecyl
sulfate-polyacrylamide gel electrophoresis and Western blotting using
CCR4 and CAF1 antibodies. Molecular weight markers for the gel
filtration experiment were blue dextran (2 × 106 Da),
thyroglobulin (0.67 × 106 Da), and bovine serum
albumin (6.6 × 104 Da). (C) Immunoprecipitations were
conducted in strain MY1737 [not1 pNOT1(396-2108)] and
wild-type backgrounds with CAF1 antibody. Lanes 1 and 2 contain 1/10 of
the crude extract (Cr. Ex.) protein input used for the
immunoprecipitations (Ip) in lanes 3 and 4. Western analysis was
conducted with anti-CCR4 and anti-NOT antibodies as indicated. NOT4 and
NOT2 proteins in the crude extracts in lanes 1 and 2 were visible in
the original Western blots and were in equal abundance for the two
strains. IgG, immunoglobulin G.
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We also conducted gel filtration analysis in not3 and
not4 backgrounds. In a not3 deletion strain, CCR4
and CAF1 still migrated in large and medium complexes but the proteins
were clearly more spread out, suggesting that their stability in the
complexes was being compromised (data not shown). A not4
deletion had no apparent effect on CCR4 or CAF1 migration in the 1.9- and 0.8-mDa complexes (data not shown). CCR4 and CAF1 can therefore
still associate in the CCR4-NOT complex in the absence of
not3, not4, or not5, although these
deletions may cause subtle effects on the structure and integrity of
the complex. It should also be mentioned that in contrast to CCR4 and
CAF1, the association of several other components of the CCR4-NOT
complex could not be determined by gel filtration chromatography. NOT2
protein was hardly detectable after Superose 6 chromatography, NOT3
tended to migrate at its monomeric size, and NOT5 and NOT1 did not tend
to migrate in well-defined peaks as was observed for CCR4 and CAF1
(data not shown).
The above results indicate that CCR4 and CAF1 can associate with NOT1
in the absence of NOT3, NOT4, or NOT5. In a not2 strain, however, the association of CCR4 with CAF1 and the NOT proteins could
not be ascertained by immunoprecipitation due to the inability to
immunoprecipitate sufficient levels of CCR4 and CAF1 proteins. This may
be partially the result of the very low amount of CAF1 and several of
the NOT proteins present in the extracts (data not shown; see also Fig.
5), but it may also result from overall instability of the complex and
susceptibility to proteolytic degradation in a not2
background. Our gel filtration analysis indicated that CCR4 still
migrated in 1.9- and 0.9-mD complexes in a not2 background (bottom panel of Fig. 2B), but the presence of CAF1 in the 0.9-mDa complex could not be determined and only a very small amount of CAF1
was visible in the 1.9-mDa complex (data not shown). In a not2-1 strain background, CCR4 and CAF1 migrated in both
1.9- and 0.9-mDa complexes (data not shown). These results suggest that
NOT2 affects the overall integrity of the complex but may not be
required for CCR4 association in the CCR4-NOT complex.
It is also apparent in Fig. 2A that when CCR4 is immunoprecipitated,
NOT4 is not required for NOT2, -3, and -5 to associate with CCR4, CAF1,
and NOT1, and similarly, NOT3 is not required for NOT2, -4, -5, to
associate with CCR4, CAF1, and NOT1. In a not5 background,
however, because of the decrease in abundance of NOT3, NOT4, and NOT2
protein levels in the crude extracts used for the immunoprecipitation
(data not shown), we could not ascertain if these three NOT proteins
associated with CCR4, CAF1, and NOT1 following the immunoprecipitation.
These results confirm that CCR4 and CAF1 are tightly if not directly
linked, that NOT3 to NOT5 are not required for CCR4 and CAF1
association or with their association with NOT1, and that neither NOT3
nor NOT4 is required for NOT2 and NOT5 association with CCR4, CAF1, and NOT1.
The C terminus of NOT1 is not required for CCR4 and CAF1
association.
We used several complementary approaches to identify
the region of NOT1 which interacted with CCR4 and CAF1. Since a
not1 deletion is lethal, we initially used two truncated
versions of NOT1 to assess the NOT1 requirement for CCR4 and CAF1
association. First, we analyzed the not1-2 allele. The
not1-2 allele results in a NOT1 protein that is about 120 kDa in size (Fig. 2A, lane 2) and has been reported to be the result of
a stop codon located in the region between residues 396 and 1318 of
NOT1 (26). About 10% of the not1-2 protein is full length,
which is apparently sufficient for the yeast to survive. The truncated
not1-2 protein still coimmunoprecipitated with either CCR4 or CAF1
(Fig. 2A, lane 2, and data not shown). However, NOT5 and NOT4 no longer immunoprecipitated with CCR4 in a not1-2 strain (Fig. 2A,
lane 2), and the amount of NOT2 was significantly reduced in the
immunoprecipitation. The reduced amount of NOT2 that
coimmunoprecipitated could be derived from NOT2 binding to the
full-length NOT1 protein (Fig. 2A, lane 2). NOT5, NOT2, and NOT4
appear, therefore, to interact with the C-terminal region of NOT1, a
result confirmed by other results described below.
Second, we examined whether the CCR4-CAF1 interaction required the
N-terminal 395 codons of NOT1. Immunoprecipitating CAF1 coimmunoprecipitated a significant amount of CCR4 in a strain carrying
NOT1(396-2108) (Fig. 2C, lane 3). The central region of NOT1 (residues
396 to about 1100) appears sufficient, therefore, for CCR4 interaction
with CAF1, although the N-terminal 395 residues of NOT1 appear to aid
the stable association of CCR4 with CAF1 (Fig. 2C; compare lane 3 with
lane 4).
An internal segment (residues 667 to 1152) of NOT1 is sufficient
for binding CCR4 and CAF1.
To examine more thoroughly the region
of NOT1 that interacted with CCR4 and CAF1, we expressed in yeast
several LexA-NOT1 fusions and determined their ability to be
coimmunoprecipitated with CCR4 and CAF1. Three LexA-NOT1 fusions,
LexA-NOT1(667-1152), LexA-NOT1(667-2108), and
LexA-NOT1(1-1152), were coimmunoprecipitated with CCR4 (Fig.
3A, lanes 6, 9, and 10) or CAF1 antibody
(data not shown). In contrast, the LexA-NOT1(1-667) and
LexA-NOT1(1490-2108) could not be coimmunoprecipitated with CCR4 or
CAF1 (Fig. 3A, lanes 7 and 8, and data not shown). Residues 667 to 1152 of NOT1 are, therefore, sufficient for binding CCR4 and CAF1, a
conclusion that agrees with the ability of CCR4 and/or CAF1 to
immunoprecipitate both the truncated not1-2 protein and
NOT1(396-2108).
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FIG. 3.
Localization of the NOT1 protein region that is
sufficient for binding CCR4. (A) LexA-NOT1(667-1152) is sufficient for
binding to CCR4 and CAF1. LexA-NOT1 fusions as indicated were expressed
in strain EGY188, and immunoprecipitations were conducted with
anti-CCR4 antibody. Western analysis was conducted with anti-LexA
antibody. The crude protein extracts in lanes 1 to 5 contain 1/10 of
the amount of extract used for the immunoprecipitations (Ip) displayed
in lanes 6 to 10, respectively. IgG, immunoglobulin G. (B) The C
terminus of NOT1 binds NOT2, NOT4, and NOT5. Strain EGY188 containing
either LexA-NOT1(1-1152) or LexA-NOT1(1490-2108) was
immunoprecipitated with LexA antibody. Western analysis using the
antibodies as indicated was conducted as detailed in Fig. 1. Cr. Ex.,
crude extract.
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The N-terminal 1318 residues of NOT1 are required for association
of CCR4 with CAF1 in the 0.9-mDa complex.
We further analyzed
CCR4-CAF1-NOT1 interactions by Superose 6 gel filtration. Removing the
N-terminal half of NOT1 (residues 1 to 1318) caused the dissociation of
CCR4 from the 0.9-mDa complex peak fractions 10 to 12 (compare Fig.
4B with Fig. 4A), suggesting that
residues 1 to 1318 of NOT1 are required for the physical integrity of
CCR4 in this complex. Very little CAF1 protein could be detected
following Superose 6 chromatography (data not shown). The total CAF1
protein level was reduced in the strain carrying NOT1(1318-2108) (Fig.
5), but that reduction alone cannot
explain the extremely low level of total CAF1 in all Superose 6 fractions. The CAF1 protein may be particularly sensitive to
degradation without the presence of the N terminus of NOT1. Deleting
the N-terminal 395 codons of NOT1 had no effect on CCR4 migration in
either the 1.9- or 0.9-mDa complex (Fig. 4C). The gel filtration
profile of CCR4 in the not1-2 strain showed that CCR4
migrated at 1.9 mDa and about 700 kDa (fractions 12 to 14). The shift
of the 0.9-mDa peak may be the result of both the truncated not1-2
protein being about 70 kDa smaller than NOT1 and the loss of the NOT5
and NOT4 proteins (Fig. 2A). CAF1 was also found to migrate in 1.9- and 0.9-mDa peaks in the not1-2 strain and in 1.9- and 0.9-mDa
complexes in the NOT1(396-2108) strain (data not
shown). These gel filtration results agree with the above
immunoprecipitation results and indicate that in order for the
CCR4-CAF1-NOT1 proteins to associate in the 0.9-mDa complex, NOT1 must
contain residues 396 to about 1100.
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FIG. 4.
Gel filtration analysis of CCR4 in NOT1
mutant backgrounds. (A) Strain KY803 (wild type); (B) strain MY1738
[not1 pNOT1(1319-2108)]; (C) strain MY1737
[not1 pNOT1(396-2108)]; (D) strain MY8
(not1-2). Gel filtration chromatography was conducted as
described for Fig. 2B. Anti-CCR4 antibody was used to detect the CCR4
protein.
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FIG. 5.
CCR4, CAF1, and NOT5 protein levels in not
mutant backgrounds. All strains were grown to mid-log phase in YEP
medium containing 5% glucose. Cells were harvested and lysed, and 40 µg of total protein was loaded in each lane. The RNA helicase homolog
DHH1 was used as an internal control to demonstrate equivalent loading
on the sodium dodecyl sulfate-polyacrylamide gel. Strains used: KY803
(wild type [wt]); MY8 (not1-2); MY1737 [not1
pNOT1(396-2108)]; MY1738 [not1
pNOT1(1319-2108)]; MY16 (not2-1); 1393-4a
(not2); MY508 (not3); MY537 (not4);
MY1735 (not5). Western blot analysis was conducted with
antibodies directed against CCR4, CAF1, NOT5, and DHH1 as indicated.
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The C-terminal region from residues 1490 to 2108 of NOT1 interacts
with NOT2, NOT4, and NOT5.
Because the C-terminal part of NOT1 was
required for NOT5, NOT4, and NOT2 to associate with CCR4, CAF1, and
NOT1 (Fig. 2A, lane 2), we initially used two-hybrid analysis to
examine interactions of LexA-NOT1(1490-2108) with the NOT components
of the CCR4-NOT complex (20). B42-NOT2, B42-NOT4, and
B42-NOT5 all interacted with LexA-NOT1(1490-2108) (410, 520, and 77 U
of -galactosidase/mg, respectively). As expected from the
immunoprecipitation analysis, neither B42-CAF1 nor B42-CCR4 interacted
with the C-terminal region of NOT1 (5.5 and 3.0 U of
-galactosidase/mg, respectively; values for B42-NOT1, B42-NOT3, and
B42 were 5.8, 4.5, and 3.2 U of -galactosidase/mg, respectively). To
further analyze the interaction of the C terminus of NOT1 with other
components of the CCR4-NOT complex, we immunoprecipitated LexA-NOT1(1-1152) and LexA-NOT1(1490-2108) with LexA antibody. As
displayed in Fig. 3B, lane 4, the C-terminal portion of
NOT1(1490-2108) was able to immunoprecipitate NOT2, NOT5, and
NOT4. In contrast, LexA-NOT1(1-1152) did not immunoprecipitate these
proteins and instead immunoprecipitated CAF1 (Fig. 3B, lane 3) and a
small amount of NOT3 (not shown). While CCR4 did not immunoprecipitate with either LexA fusion, in Fig. 3A it clearly interacted with residues
667 to 1152 to NOT1. The above immunoprecipitation, gel filtration, and
two-hybrid analysis indicate, therefore, that the NOT1 protein contains
two separable domains, 667 to 1152 for binding CAF1 and CCR4 and 1490 to 2108 for interacting with NOT2, NOT4, and NOT5.
The effects of deleting the different regions of NOT1 on
ADH2 expression were subsequently analyzed. NOT1(1318-2108)
resulted in a two- to threefold decrease in ADH II activity compared to NOT1(396-2108) or full-length NOT1 (Table
2). LexA-NOT1(1490-2108) resulted in a
similar low level of ADH2 expression (Table 2). Coexpressing
in yeast LexA-NOT1(1-1152) along with NOT1(1318-2108) allowed a
twofold increase in ADH II activity. In contrast, coexpressing LexA-NOT1(1-667) was insufficient for recovering the ability of NOT1(1318-2108) to fully activate ADH2. The 667-1152
region of NOT1 that binds CAF1 and CCR4 appears, therefore, to be
necessary for recovering in trans NOT1(1318-2108) function
and confirms the existence of two distinct functional regions of NOT1.
NOT2 and NOT5 associate closely and in the absence of CAF1, NOT3,
or NOT4.
NOT5-NOT2 interactions were also analyzed following the
observation that when LexA-NOT5 is immunoprecipitated with anti-LexA antibody, all components of the CCR4-NOT complex can be
coimmunoprecipitated (Fig. 6A, lane 1).
Immunoprecipitation of LexA alone does not coimmunoprecipitate any of
these proteins (reference 20 and data not shown),
indicating that it is the NOT5 moiety which is interacting with these
proteins. As shown in Fig. 6A, lanes 2 to 4, NOT2 was capable of
immunoprecipitating with LexA-NOT5 in the absence of CAF1, NOT3, or
NOT4. As expected no CCR4 was capable of coimmunoprecipitating with
LexA-NOT5 in the absence of CAF1 (Fig. 6A, lane 2). It should be noted
that in the original results (Fig. 6A, lane 3) some CCR4 protein was
immunoprecipitated with LexA-NOT5 in a not3 strain. These
results are in agreement with the physical separation of CAF1 and CCR4
from the NOT2 and NOT5 proteins and the dependency on CAF1 for CCR4
association with these other factors. Moreover, NOT3 and NOT4 had no
effect on the ability of LexA-NOT5 to coimmunoprecipitate CAF1, NOT2,
or NOT1, although NOT3 may play a role in stabilizing CCR4 interactions with the complex. We subsequently used anti-NOT5 antibody to analyze more completely the NOT5-NOT2 association. Anti-NOT5 antibody immunoprecipitated only NOT5, NOT2, and a small amount of NOT1 (Fig.
6B, lane 2). While the NOT5 antibody may interfere with the association
of NOT5 with the rest of the CCR4-NOT protein components, its ability
to immunoprecipitate NOT2 confirms a close physical association of NOT2
and NOT5.
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FIG. 6.
NOT5 coimmunoprecipitates with NOT2 in the absence of
CAF1, NOT3, and NOT4. (A) LexA-NOT5 immunoprecipitates NOT2 in the
absence of CAF1, NOT3, and NOT4. Immunoprecipitations (Ip) were
conducted with anti-LexA antibody, and Western analysis used antibodies
as indicated; LexA-NOT5 is full-length NOT5 fused to LexA(1-202).
Lanes: 1, KY803 (wild type [wt]); 2, KY803-c1 (caf1); 3, MY508 (not3); 4, MY537 (not4). In the original
Western blots, CCR4 was immunoprecipitated in lane 3. (B) NOT5 antibody
immunoprecipitates NOT2. Antibody against CCR4 (lane 1) or NOT5 (lane
2) was used for immunoprecipitations from strain KY803. (C) NOT3
immunoprecipitates NOT1, NOT2, and NOT5 in the absence of CCR4, CAF1,
and NOT4. Anti-NOT3 antibody was used to conduct the
immunoprecipitations. WT (wild type), strain KY803; ccr4,
KY803-1; caf1, KY803-c1; not4, MY537. Western
analysis was conducted as detailed above.
|
|
NOT3 associates with the CCR4-NOT complex independently of CCR4,
CAF1, or NOT4.
Immunoprecipitating NOT3 was also found to
coimmunoprecipitate the whole CCR4-NOT complex (Fig. 6C, lane 1). We
therefore investigated the effects of various deletions in CCR4-NOT
components on NOT3 immunoprecipitation of the complex. Deleting
CCR4 had no effect on NOT3 associations (Fig. 6C, lane 2),
whereas caf1, as expected, resulted in only CCR4 not being
able to associate in the complex (lane 3). Deleting NOT4 also had no
effect on NOT3 interaction with the other components of the complex
(Fig. 6C, lane 4). In not1-2, not2, or
not5 strains, NOT3 could not be immunoprecipitated, suggesting that NOT2, NOT5, and the C-terminal region of NOT1 are
required for stable NOT3 association with the rest of the complex or
existence in an immunoprecipitable form.
CAF1 and CCR4 can act phenotypically opposite NOT2, NOT4, and
NOT5.
Previously we had shown that a caf1 or
ccr4 deletion resulted in no or very little increased 3-AT
resistance (20) whereas mutation or deletion of the
NOT genes is known to cause increased 3-AT resistance,
indicative of increased HIS3 gene expression (6,
23). The not4 and not5 deletions also
resulted in increased ADR1-5C activation of
ADH2 under glucose growth conditions (ADH II activities of
370 ± 24 and 220 ± 10 mU/mg, respectively, versus 94 ± 7.6 mU/mg for ADR1-5C), whereas a
caf1 deletion had no effect on
ADR1-5C activation of ADH2 and a
ccr4 deletion reduced twofold the ability of
ADR1-5C to activate (ADH II activities of
95 ± 7.4 and 45 ± 1.4 mU/mg, respectively). Similar
differences between the effects of caf1 and ccr4
effects on gene expression and the effects of the not alleles were reported previously (20). The most salient of
these is the reduction in HO-lacZ and FKS1-lacZ
expression caused by ccr4 and caf1 alleles and
the two- to threefold increases in HO-lacZ or
FKS1-lacZ expression caused by not1-2,
not2, and not4 defects (20). These
phenotypic effects support the existence of the separate location of
these groups of proteins within the CCR4-NOT complex.
Since deleting NOT1 is lethal, we examined the effects of
deleting components from the two separate groups of proteins in the
CCR4-NOT complex. Suitable crosses were made between either ccr4 or caf1 deletions and not
deletions, and the viability of different deletion combinations was
analyzed by tetrad analysis. As shown in Table
3, not2 and not5
were lethal in combination with either ccr4 or
caf1. Lethality was confirmed in all cases by ascertaining
whether a plasmid-borne copy of one of the deleted genes could rescue
the lethality. In addition, in all cases where the lethality was
rescued by the plasmid-borne gene, the plasmid could not be lost from
the cell, confirming the lethality of the double deletion. These
synthetic lethalities are consistent with the importance of NOT2 and
NOT5 to the integrity and function of the CCR4-NOT complex and to a
role that is in addition to and/or separate from CCR4 and CAF1. Whereas
deleting not3 did not result in synthetic phenotypes with
either caf1 or ccr4, the not3-2
mutation clearly resulted in exacerbated growth phenotypes with
ccr4 (Table 3). not1-2 also displayed synthetic
growth defects with a ccr4 or caf1 deletion
(Table 3), consistent with the observation that in a not1-2
strain, NOT2, NOT4, and NOT5 associate in the complex less well due to
the increased levels of C-terminally truncated NOT1 protein (Fig. 2A,
lane 2).
The hallmark of the not alleles is their increased
resistance to 3-AT, yet the ccr4 and caf1 alleles
do not display this phenotype (20). Because of the possible
antagonistic behavior of CCR4 and CAF1 in relation to the other NOT
proteins, we tested the effect of a ccr4 or caf1
deletion on the ability of not alleles to confer increased
3-AT resistance. We observed that a caf1 or ccr4
deletion suppressed the increased 3-AT resistance of not1-2, not3-2, and not4 alleles (Table
4), confirming that CCR4 and CAF1 can act
in an opposite manner to the NOT proteins in certain promoter contexts.
| |
DISCUSSION |
CCR4-CAF1 interact with the N-terminal 1152 residues of NOT1,
whereas NOT2, NOT4, and NOT5 interact with the C-terminal 1490-2108
region of NOT1.
It was shown previously that disrupting the
CAF1 gene blocked the ability of CCR4 to associate with NOT1
(20). In this report, we showed that CAF1 is required for
CCR4 to associate with all of the NOT proteins. NOT3,
NOT4, and NOT5 were, in turn, found not to be
required for CCR4-CAF1-NOT1 association or for CCR4 and CAF1
association in the 1-mDa complex. Relatedly, immunoprecipitating NOT3
or LexA-NOT5 did not coimmunoprecipitate CCR4 when CAF1 was deleted. These results clearly indicate that CCR4 binds through CAF1 to
associate with NOT1 and the other components of the complex (Fig.
7 summarizes the interactions in the
CCR4-NOT complex).
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|
FIG. 7.
Model for protein contacts in the CCR4-NOT complex.
Based on the results presented herein, CAF1 is presumed to bind to
residues 667 to 1152 of NOT1, CCR4 binds to CAF1, and NOT2 and NOT5
interact with the C-terminal residues 1490 to 2108 of NOT1 in no
particular order. NOT4 is placed on the periphery of NOT2 and NOT5, and
it is presumed that NOT3 makes contacts with both NOT2, NOT5, or NOT4
and the N terminus of NOT1.
|
|
The region of NOT1 with which CCR4 and CAF1 physically associate was
found to be distinct from that bound by the NOT2, NOT4, and NOT5
proteins. Several lines of evidence indicate that the region of NOT1
binding CAF1 is localized to residues 667 to 1152. First, CCR4 or CAF1
could immunoprecipitate an internal segment of NOT1 (residues 667 to
1152). Second, when the immunoprecipitation was conducted in the
reverse direction, LexA-NOT1(1-1152) immunoprecipitated CAF1 but
LexA-NOT1(1490-2108) did not. Third, in a not1-2 strain wherein the major NOT1 species contains only the N-terminal 1,000 residues or so of NOT1, both CCR4 and CAF1 immunoprecipitated with the
not1-2 protein. Fourth, removing the N-terminal 395 residues of NOT1
did not abrogate the ability of CAF1 to immunoprecipitate CCR4,
although the N-terminal segment of NOT1 clearly played some role in
stabilizing the CCR4-CAF1 interactions. Finally, when the N-terminal
1,318 residues of NOT1 were removed, neither CCR4 nor CAF1 was able to
associate in the 1-mDa complex.
In contrast to the above results, the region of NOT1 that associates
with NOT2, NOT4, and NOT5 was localized to the C-terminal portion of
NOT1 (residues 1490 to 2108). The NOT2, NOT4, and NOT5 were found to
display two-hybrid interactions with LexA-NOT1(1490-2108), and
immunoprecipitating LexA-NOT1(1490-2108) coimmunoprecipitated NOT2, NOT4, and NOT5. As a comparison, immunoprecipitating
LexA-NOT1(1-1152) failed to coimmunoprecipitate these proteins.
Moreover, in the not1-2 strain, NOT5 and NOT4 did not
immunoprecipitate with CCR4 or CAF1 and only a limited amount of NOT2
coimmunoprecipitated (possibly due to association with the residual
full-length NOT1 still present in the cell). Finally, NOT2, NOT4, and
NOT5 were coimmunoprecipitated in the absence of CAF1 when either NOT3
or LexA-NOT5 was immunoprecipitated. These results indicate that it is
the C-terminal portion of NOT1 protein (residues 1490 to 2108) that
binds NOT2, NOT4, and NOT5. These data establish a clear physical
separation of CCR4 and CAF1 from NOT2, NOT4, and NOT5 through their
binding to separate regions of NOT1. Other limited interactions between
these two groups of proteins can not be excluded, however.
Our data further show that NOT2 and NOT5 are closely linked. First,
deletion of either of these components tends to result in decreased
abundance of several other components in the complex. NOT2 and NOT5
appear to have general effects on the integrity or stability of the
CCR4-NOT complex. Second, both proteins interacted in the two-hybrid
system with the C-terminal segment of NOT1 and immunoprecipitated with
the same segment of NOT1. Third, NOT3, NOT4, CAF1, or CCR4 defects did
not affect the ability of LexA-NOT5 to immunoprecipitate NOT2. Fourth,
NOT5 antibody coimmunoprecipitated NOT2, some NOT1, and no other
CCR4-NOT component. These data implicate a close physical association
between NOT2 and NOT5 that is important to the stability of the
CCR4-NOT complex.
While NOT3 and NOT4 appear to be peripheral to NOT2 and NOT5, the
location of the NOT3 protein could not be readily determined. For one
thing, in all mutant strains that we analyzed by gel filtration analysis, NOT3 migrated at or near its monomeric size. NOT3 appears to
be less stably associated with the CCR4-NOT complex.
Immunoprecipitating CCR4 and CAF1 showed that NOT3 failed to
coimmunoprecipitate in a not1-2 strain, suggesting NOT3
associated with the C terminus of NOT1. However, when
LexA-NOT1(1-1152) was immunoprecipitated, a small and
reproducible amount of NOT3 was coimmunoprecipitated. No NOT3 was
observed to coimmunoprecipitate with LexA-NOT1(1490-2108). Also,
NOT3 did not require NOT4 for association with NOT1, CCR4, or CAF1.
Since neither a not3 nor a not4 deletion affected
the ability of LexA-NOT5 to immunoprecipitate NOT1, CCR4, CAF1,
or NOT2, it appears that NOT3 and NOT4 are peripheral to NOT2 and NOT5.
However, a not3 deletion did reduce the ability of LexA-NOT5 to immunoprecipitate CCR4. In Fig. 7, we therefore assign NOT3 a place
that includes contacts to the N terminus of NOT1 and binding to the
outskirts of NOT2 and NOT5.
In our model for the physical arrangement of the components of the
CCR4-NOT complex based on the above data (Fig. 7), CCR4 associates at
one end of the complex through binding CAF1, which in turn binds the
central portion of NOT1 (residues 667 to 1152). NOT2 and NOT5 bind the
C-terminal region of NOT1 (residues 1490 to 2108). NOT4 is on the
outside of NOT2 and NOT5. NOT3 may display multiple contacts both to
the N terminus of NOT1 and to NOT2 and NOT5.
CCR4 and CAF1 differ phenotypically from NOT2 to NOT5.
The
above biochemical data define CCR4 and CAF1 as a separate group of
proteins within the CCR4-NOT complex that contacts the NOT1 protein in
a distinct location from the NOT2, NOT4, and NOT5 proteins. Based on
these identified separate locations within the complex, we would expect
these subgroups of proteins to exhibit specific differences in both
function and the proteins with which they interact. Phenotypically,
CCR4 and CAF1 can display a number of functions that are different from
those displayed by the other NOT proteins. This distinction correlates
with the above-defined physical interactions. First, the NOT1 protein
[NOT1(1490-2108)] which lacks the binding site for CAF1 and CCR4 is
defective in ADH2 derepression. Adding back to yeast in
trans the N-terminal segment of NOT1 (residues 1 to 1152)
can rescue this defect in ADH2 expression, implicating the
binding of CAF1 and CCR4 to this region as important for full
ADH2 expression. Second, the not4 and
not5 disruptions augment
ADR1-5C-induced ADH2 expression under
glucose growth conditions, whereas caf1 has no effect and
ccr4 causes a reduction in expression. Third, at other
promoters such as HO-lacZ and FKS1-lacZ, the
not1, not2, and not4 defects
(not5 was not tested) result in increased expression whereas
caf1 and ccr4 result in defects in expression (20). Fourth, the not alleles were identified in
a genetic screen for increased 3-AT resistance. In contrast, little or
no effect on 3-AT resistance is observed for caf1 or
ccr4 defects (20). Fifth, whereas not
alleles cause increased 3-AT resistance, ccr4 and
caf1 defects can suppress these effects.
In addition, the ccr4 and caf1 defects when
combined with not alleles resulted in synthetic phenotypes.
ccr4 or caf1 were lethal with either
not2 or not5 deletions, whereas ccr4
caf1 and not2 not5 double knockouts are viable.
Although other explanations are possible with respect to synthetic
growth defects, the synthetic defect of ccr4 and
caf1 with that of not2 and not5 is
consistent with the idea that these two groups of proteins display
separate functions that are important for the overall integrity and
activity of the CCR4-NOT complex. It is also possible that NOT2 and
NOT5 display functions redundant with those of CCR4 and CAF1, although we feel that this is unlikely because of their dissimilarity in protein
sequence and their actual physical separation and distinctiveness within the CCR4-NOT complex. Similarly, ccr4 not1-2 and
caf1 not1-2 knockouts also displayed synthetic phenotypes.
not1-2 results from a stop codon (26) that causes
90% of the NOT1 protein to be about 1,100 amino acids long, which
confirms that loss of the C terminus of the not1-2 protein in
combination with ccr4 or caf1 defects results in
a synthetic phenotype. The nonlethality of this combination is most
likely due to the existence of some full-length NOT1 protein. These
data also suggest that the lethality that results from deleting the
not1 gene may be caused by the combined loss of essential
parts of the CCR4-CAF1 components and the NOT2 to NOT5 components. NOT1
may, therefore, be an essential protein due to its structural role in
forming and maintaining the CCR4-NOT complex. However, the C-terminal
region of NOT1 (residues 1490 to 2108) encompassing the site of binding
NOT2, -4, and -5 by itself can complement a not1 disruption,
unlike the region of NOT1 binding CCR4 and CAF1 (residues 667 to 1152).
The C terminus of NOT1 may be essential due to its ability to bind
multiple NOT proteins, and/or the C terminus of NOT1 conveys another,
as yet undetermined essential function.
It should also be noted that not4 or not3
deletions in combination with ccr4 or caf1 did
not result in synthetic phenotypes. Therefore, although NOT2 and NOT5
appear important to the integrity of the complex, the lethality between
not2 or not5 and that of ccr4 or
caf1 is not simply due to loss of structural roles for NOT2
and NOT5 and their presumed importance for binding NOT3 and NOT4.
Instead, NOT2 and NOT5 must play an important biochemical role
independent of their mere physical presence in the CCR4-NOT complex.
The observation that not3 and not4 deletions do
not display synthetic growth defects with that of ccr4 and
caf1 suggest either that these proteins as a group are not
required for the function of any essential genes or that they actually
function in the same pathway. It should be noted, though, that the
not3-2 allele in combination with ccr4 resulted
in a synthetic growth defect, suggesting that the not3-2 protein
affects a particular interaction in a negative manner that is worse
than the complete loss of the NOT3 protein.
Roles of the 1.9- and 0.9-mDa CCR4-NOT complexes.
CCR4, CAF1,
NOT1, NOT3, and NOT5 have all been found to associate in 1.9- and
0.9-mDa complexes (reference 20 and results herein),
and NOT2 has also been shown to migrate at 0.9-mDa (unpublished observation). The association of CCR4 in the 0.9-mDa complex requires CAF1 (20) and, as we have shown here, the N-terminal region of NOT1. A caf1 deletion reduced significantly the ability
of CCR4 to associate in the 1.9-mDa complex (20) but did not
eliminate it entirely. CCR4 must, therefore, be able to interact in the 1.9-mDa complex independently of CAF1 or its association with NOT1. The
contacts and function for CCR4 in the 1.9-mDa complex may be separable
from or additional to those it displays in the 0.9-mDa complex.
Relatedly, CCR4 must express a function separate from its presence in
the 0.9-mDa complex since a ccr4 deletion was lethal when
combined with the strain expressing only pNOT1(1490-2108). It remains
possible that CCR4 exists in multiple 1.9-mDa complexes (3).
Other proteins that have been found to associate with CCR4, CAF1, or
NOT proteins are DHH1 (15), CAF4, CAF16 (21),
DBF2 (22), and MOB1 (18). These proteins may all
be candidates for components of the 1.9-mDa complex. DHH1, CAF16, and
MOB1 (3a) do not immunoprecipitate with CCR4 and are not
components of the 0.9-mDa complex. However, CAF16 (21),
DBF2, and MOB1 (unpublished observation) have been found to migrate in
a 1.9-mDa complex. The complete components, assembly, and functional
significance of the two CCR4-NOT complexes remain to be clarified.
Characterizing the 1.9-mDa complex, understanding how the CCR4-NOT
complexes interact with other transcriptional factors, and defining the particular roles of CCR4 and CAF1 in contrast to NOT2, NOT5, NOT3, and
NOT4 should lead to a better conception of how the CCR4-NOT proteins
function in both activated and repressed transcription.
This research was supported by NIH grant GM41215, NSF grant
MCB95-13412, and HATCH project H291 to C.L.D. and Swiss National Science Foundation grant 31-49808.96 to M.A.C.
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Abstract
Introduction
Scientific contribution no. 1999 from the New Hampshire
Agricultural Experiment Station.
