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Molecular and Cellular Biology, June 2000, p. 3843-3851, Vol. 20, No. 11
0270-7306/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.
Repression of Ribosome and tRNA Synthesis in Secretion-Defective
Cells Is Signaled by a Novel Branch of the Cell Integrity
Pathway
Yun
Li,1
Robyn D.
Moir,1
Indra K.
Sethy-Coraci,1,
Jonathan R.
Warner,2 and
Ian M.
Willis1,*
Departments of
Biochemistry1 and Cell
Biology,2 Albert Einstein College of Medicine,
Bronx, New York 10461
Received 12 January 2000/Returned for modification 14 February
2000/Accepted 8 March 2000
 |
ABSTRACT |
The transcription of ribosomal DNA, ribosomal protein (RP) genes,
and 5S and tRNA genes by RNA polymerases (Pols) I, II, and III,
respectively, is rapidly and coordinately repressed upon interruption
of the secretory pathway in Saccharomyces cerevisiae. We
find that repression of ribosome and tRNA synthesis in
secretion-defective cells involves activation of the cell integrity
pathway. Transcriptional repression requires the upstream components of
this pathway, including the Wsc family of putative plasma membrane
sensors and protein kinase C (PKC), but not the downstream
Bck1-Mkk1/2-Slt2 mitogen-activated protein kinase cascade. These
findings reveal a novel PKC effector pathway that controls more than
85% of nuclear transcription. It is proposed that the coordination of
ribosome and tRNA synthesis with cell growth may be achieved, in part,
by monitoring the turgor pressure of the cell.
 |
INTRODUCTION |
The production of ribosomes and
associated protein-synthetic machinery consumes substantial amounts of
metabolic energy. It is estimated that yeast cells growing with a
generation time of about 100 min devote at least 60% of their total
nuclear transcription to the synthesis of the large rRNAs by RNA
polymerase (Pol) I and as much as 50% of the initiation events by Pol
II to the transcription of ribosomal protein (RP) genes
(30). This level of transcription is needed to sustain the
production of some 2,000 ribosomes per min and allow the doubling of
the cell's ribosome content during each cell cycle. The large
investment of high-energy phosphate in ribosome synthesis provides a
biological rationale for the evolution of mechanisms that safeguard the
cell's metabolic economy. These mechanisms couple the synthesis of
ribosomes and ribosomal substrates, such as tRNAs, with the
protein-synthetic needs of the cell and the availability of nutrients
and/or growth factors (33, 35).
A potentially important mechanism in higher eukaryotic cells that may
help to achieve metabolic economy and coordinate protein-synthetic capacity with cell growth involves transcriptional repression of Pols I
and III by the tumor suppressor protein Rb (32). This activity of Rb results from its inhibition of preinitiation complex assembly and/or function through direct binding of the Pol I- and Pol
III-specific transcription factors UBF and TFIIIB, respectively (2, 3, 15, 29, 34). In addition to Rb and the related pocket
proteins, p107 and p130 (27), other mechanisms for
controlling transcription of the protein-synthesizing machinery appear
to exist. In yeast cells, for example, the production of ribosomal components and tRNAs in response to nutrient availability and growth
rate is regulated predominantly at the transcriptional level in the
absence of an Rb homolog (11, 24, 33, 35). These
observations suggest that yeast may be a good model system in which to
examine the fundamental mechanisms coordinating ribosome synthesis with
cell growth.
In the past several years, studies with Saccharomyces
cerevisiae have uncovered a regulatory circuit that connects the
synthesis of the large rRNAs and RPs with the secretory pathway
(18, 20, 21). These studies have shown that interruption of
the secretory pathway at various points, from peptide insertion into
the endoplasmic reticulum (ER) to vesicle fusion with the plasma
membrane, causes transcriptional repression of ribosomal DNA (rDNA) and
RP genes. The intracellular signaling pathway mediating this response
does not involve any of the common mechanisms known to regulate
ribosome biosynthesis and is distinct from the pathway that monitors
protein folding in the ER (21, 22). However, continued
protein synthesis and protein kinase C (PKC) are both required for
repression in secretion-defective cells (21, 22). These
findings, together with the fact that repression of RP genes can be
induced by chlorpromazine, an agent that causes membrane stretching,
provide the current working model for signal transduction in this
system (22). It is proposed that a failure of the secretory
pathway leads to an insufficiency in the supply of lipids and proteins
which are needed for growth of the plasma membrane and cell wall
synthesis. In the absence of plasma membrane growth, continued protein
synthesis is thought to create a higher-than-normal intracellular
pressure (turgor), effectively stretching the plasma membrane. This
perturbation of the plasma membrane is suggested to activate a
PKC-dependent cell integrity pathway leading to transcriptional
repression of ribosome synthesis. Activation of the
PKC-mitogen-activated protein (MAP) kinase cell integrity pathway
following an increase in the osmotic gradient across the plasma
membrane (high inside, low outside) is well documented (8).
However, the role of this pathway in repressing rRNA and RP gene
transcription in secretion-blocked cells has not yet been fully explored.
To date, neither the synthesis of the 5S rRNA component of the ribosome
nor that of the tRNA adapter molecules of protein synthesis has been
examined in secretion-blocked cells. Given the likelihood that these
Pol III transcripts are coregulated with ribosome synthesis and the
possibility that a common signaling pathway might control transcription
by Pols I and III, as well as 50% of the activity of Pol II, we
decided to investigate this issue. We show here that transcription of
5S rRNA and tRNA genes by Pol III is indeed coordinately repressed with
transcription of RP genes in secretion-defective cells. In addition, we
find that transcriptional repression of RP and tRNA genes under these conditions is signaled by a novel branch of the cell integrity pathway
that includes plasma membrane sensors of the Wsc family and PKC but not
the downstream MAP kinase cascade.
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MATERIALS AND METHODS |
Yeast strains and growth conditions.
Yeast strains used in
this work are listed in Table 1. W303
and its congenic derivatives (312 and 169ts), strain 1783 and its
congenic derivative (DL252), the KM0XX strains (where X is any number),
and strain AC2c9 were all grown in yeast-peptone-dextrose (YPD). MN and
ALH strains were grown in YPD containing 1 M sorbitol. Strain YK193 and
its isogenic wild-type derivative (containing pFL44-SLT2-HA) were grown
in synthetic complete (SC) minimal medium lacking uracil. Tunicamycin
(Sigma) was dissolved at 5 mg/ml in 75% methanol and used at a final
concentration of 2.5 µg/ml.
Northern analysis and quantitation of RNA levels.
Total RNA
was extracted by glass-bead disruption in the presence of hot phenol
(23). For Northern analysis of tRNA precursors, RNA (20 µg) was resolved on 10% polyacrylamide-8.3 M urea gels in
Tris-borate-EDTA (TBE) buffer. After electrophoresis, gels were soaked
for 10 min in 0.5× TBE-1 µg of ethidium bromide/ml prior to digital
photography (Alpha Innotech). The RNA was then electrophoretically
transferred (in 0.5× TBE at 100 V for 2 h at 4°C) to Nytran
Plus membranes (Schleicher & Schuell) using a Bio-Rad Transfer
apparatus. After transfer, membranes were dried for 10 min and the RNA
was cross-linked by UV irradiation (0.2 J/cm). For Northern analysis of
mRNAs, total RNA (10 µg) was electrophoresed on 1.5% agarose gels
containing 6% formaldehyde (21). Capillary transfer of the
RNA to Nytran Plus membranes was performed using 20× SSC (1× SSC is
0.15 M NaCl plus 0.015 M sodium citrate) and was followed by UV
cross-linking as described above. [32P]-labeled
oligonucleotide probes were prepared as described previously (26) for detecting all tRNA precursors, TCM1 and
CYH2 mRNAs, U4 snRNA, and U3 small nucleolar RNA (snRNA)
(probe sequences are available upon request). KAR2 and
ACT1 mRNA probes were prepared by random priming and runoff
transcription, respectively (22). Hybridization and washing
of blots probed with [32P]-labeled oligonucleotides were
performed at 37°C (except for TCM1 and CYH2
[42°C]) as described previously (26). In addition, two
30-min posthybridization washes were performed in 2× SSC-0.1% sodium
dodecyl sulfate (SDS). Random-primed DNA and antisense RNA probes were
used as described by Mizuta and Warner (21). Hybridization
was detected using phosphor storage plates and a phosphorimager
(Molecular Dynamics). Signal intensities were quantified using
ImageQuant software (Molecular Dynamics). Briefly, lines one lane wide
were analyzed using a peak finder to determine the area under each
curve. These data were normalized for variations in loading using
mature tRNA levels quantified by a peak finder from digital images of
ethidium bromide-stained gels. Normalized signal intensities were
expressed relative to the values obtained at the permissive temperature
or prior to the addition of tunicamycin.
In vivo labeling.
Log-phase cultures
(A600, 0.4 to 0.7) were grown in low-phosphate
YPD at 23°C and shifted to 37°C. At various times before and after
the temperature shift, 1 ml of cells was removed to tubes containing
150 µCi of carrier-free [32P]orthophosphate for a
further 5-min incubation. Cells were harvested rapidly and frozen prior
to the preparation of total RNA (23). RNA (5 µg) was
resolved on 10% denaturing polyacrylamide gels (see above) which were
fixed, dried, and exposed to phosphor storage plates.
Western analysis.
Whole-cell lysates were prepared by
glass-bead breakage into radioimmunoprecipitation assay (RIPA) buffer
containing protease inhibitors (26). Equal amounts of the
extracts (normalized by cell number) were analyzed by Western blotting
(26) using a rabbit polyclonal antibody specific for the
doubly phosphorylated tripeptide, phosphothreonine-glutamic
acid-phosphotyrosine, found in activated Slt2 (New England Biolabs)
(28). The product specifications report no reactivity with
as much as 4 µg of unphosphorylated MAP kinase. Antibody-antigen
complexes were detected using the recommended horseradish
peroxidase-conjugated secondary antibody and enhanced chemiluminescence
(Amersham). Antibodies to TATA-binding protein (TBP) were used as a
loading control (26).
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RESULTS |
Inhibition of Pol III gene transcription in secretion-blocked
cells.
To determine whether the transcription of tRNA genes
exhibit a dependence on the secretory pathway similar to that seen for rDNA and RP genes, Northern blots of total RNA from a wild-type strain
and two temperature-sensitive strains with secretory mutations (ypt6-1 and sly1-1) were hybridized with 5'
flank- or intron-specific precursor tRNA probes. These probes detect
very short lived tRNA precursors (1), and the resulting
hybridization signals provide a reliable measure of Pol III
transcription on these genes (4, 26). At the nonpermissive
temperature, the ypt6-1 and sly1-1 mutations
cause repression of rDNA and RP gene transcription (18, 21).
YPT6 encodes a homolog of the human GTPase Rab6 and
functions in yeast in ER-to-Golgi complex transport or
cis-to-medial-Golgi complex transport. The SLY1
gene product is essential for protein and vesicle trafficking between
the ER and the Golgi complex (12). The two mutant strains
and a congenic wild-type strain were grown to mid-log phase at 23°C
and then shifted to 37°C, the nonpermissive temperature. At various
times before and after the temperature shift, cells were harvested and
frozen rapidly to preserve the tRNA precursors.
In wild-type cells, the levels of 5' flank- or intron-containing
precursors for three tRNA genes were relatively unaffected
at 37°C
(Fig.
1A). However, in both secretory
mutant strains,
the same tRNA precursors were progressively and
substantially
reduced. By 90 min, most of the tRNA precursors had
decreased
to 5 to 10% of the level prior to the temperature shift.
These
changes occurred in the absence of changes in the steady-state
levels of small RNAs including 5.8S rRNA, 5S rRNA, and mature
tRNAs (as
determined by quantitative image analysis of ethidium
bromide-stained
gels [data not shown]) and the Pol II-transcribed
U4 snRNA (Fig.
1A).
As reflected by the precursor tRNA levels,
the reduction in Pol III
transcription was very rapid; 50% inhibition
of precursor tRNA
synthesis was achieved in about 20 min (for
an example, see Fig.
4B).
Similar results have been obtained for
other tRNA genes and are
presumably representative of the entire
tRNA gene family. Thus, as for
the transcription of rDNA and RP
genes by Pols I and II, respectively,
continued transcription
of tRNA genes by Pol III requires a functional
secretory pathway.

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FIG. 1.
Inhibition of Pol III transcription in secretion-blocked
cells. (A) Northern blots of RNA (20 µg/lane) from a wild-type strain
(W303 ) and two temperature-sensitive secretory mutant strains
(containing a ypt6-1 or sly1-1 mutation) are
shown before, and at various times after, a shift from 23°C to the
nonpermissive temperature of 37°C. Blots were probed sequentially
with tRNA precursor-specific oligonucleotides and a U4 snRNA control
oligonucleotide. The tRNALeu probe detects only 5'
flank-containing precursors, whereas the tRNAIle and
tRNALys probes detect intron-containing precursors. Data
were quantified using a phosphorimager and ImageQuant software as
described in Materials and Methods. (B) In vivo [32P]
labeling of RNA in secretory and TFIIIC mutant strains. Strains growing
in low-phosphate medium were pulse-labeled for 5 min with
[32P]orthophosphate at 23°C and at the indicated times
after the shift to 37°C. Lanes 1 to 5 and 6 to 10 show the RNAs
labeled in wild-type (W303 ) and ypt6-1 strains,
respectively. Loading of equal amounts of RNA (5 µg) in each lane was
confirmed by staining with ethidium bromide prior to drying of the gel.
The RNAs labeled in a temperature-sensitive TFIIIC mutant strain, AC2c9
(lanes 11 to 13), are compared with the negative image of the ethidium
bromide-stained gel (lanes 14 to 16).
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In contrast to tRNA precursors, the other major Pol III transcription
product in yeast, 5S rRNA, has a long half-life and
undergoes minimal
processing. Therefore, the transcription of
5S rRNA genes was monitored
by pulse-labeling with [
32P]orthophosphate. Log-phase
cells from a wild-type strain, a secretory
mutant strain (the
ypt6-1 mutation), and a strain containing a
temperature
sensitive mutation in the second-largest subunit of
TFIIIC were
incubated for 5 min with [
32P]orthophosphate at the
permissive temperature. This results in
heavy labeling of bands
corresponding to 5S rRNA and mature tRNA
(Fig.
1B; compare lanes 1, 6, and 11 to lane 14). In the TFIIIC
mutant strain, decreased Pol III
transcription following a shift
to the nonpermissive temperature
reduces the labeling of these
and other bands (primarily tRNA
precursors [Fig.
1B, lanes 11
to 13]). In the wild-type strain, no
reduction in RNA labeling
is seen up to 90 min after the temperature
shift (Fig.
1B, lanes
1 to 5). Conversely, in the
ypt6-1
strain, labeling of 5S rRNA
is severely reduced after 60 and 90 min at
the nonpermissive temperature
(Fig.
1B, lanes 9 and 10). Reduced
labeling of tRNA precursors
and mature tRNA is also seen at these
times. Thus, the secretory
pathway impacts the transcription of all the
RNA components of
the ribosome. Moreover, as demonstrated by both
Northern analysis
and pulse-labeling, the consequences of interrupting
the secretory
pathway go beyond transcriptional repression of ribosomal
components
to include ribosomal substrates, namely,
tRNAs.
Coordinate repression of tRNA and RP gene transcription.
The
use of temperature-sensitive strains to study cellular processes can
sometimes lead to unanticipated synergistic interactions resulting from
the simultaneous change in temperature and loss of protein function. To
avoid this possibility, Pol III transcription was examined in cells
treated with tunicamycin, which interferes with the secretory pathway
by inhibiting the glycosylation of proteins in the ER. Addition of
tunicamycin to an early-log-phase culture of a wild-type strain
inhibited Pol III transcription, as demonstrated by a reduction in the
level of leucine precursor tRNA (Fig.
2A). This effect of tunicamycin was
delayed compared to that in secretory mutant strains. However, the
gradual induction of KAR2 (a marker for the unfolded protein
response pathway), which peaks at 90 min, suggests that the delay in
repression reflects the slower kinetics of the drug-induced secretory
block relative to secretory pathway mutations (14). Despite
the delay in achieving inhibition of the secretory pathway, image
analysis revealed that a 50% reduction in precursor
tRNALeu synthesis occurred within one cell division (Fig.
2B). Four hours after tunicamycin addition, the level of precursor
tRNALeu was 10 to 15% of the level prior to addition of
the drug. A similar end point was reached with conditional secretory
pathway mutations (Fig. 1A and 4B; also data not shown). Thus, the
dependence of Pol III transcription on a functional secretory pathway
is demonstrated by two independent methods: conditional mutations in
the pathway and an inhibitor of secretory protein processing.

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FIG. 2.
Coordinate repression of RP and tRNA gene transcription
in tunicamycin-treated cells. Tunicamycin was added to a mid-log-phase
culture of a wild-type strain (W303 ) growing at 30°C. Cells were
harvested at the indicated times for the preparation of total RNA. (A)
Northern blots were hybridized to probes specific for actin
(ACT1), ribosomal protein (TCM1 and
CYH2), KAR2, 5' flanked pre-tRNALeu
(pre-Leu), or U3 snoRNA. (B) Quantitation of RP mRNA and
pre-tRNALeu levels. Digital images of the blots from panel
A were quantified using the ImageQuant line peak finder. Integrated
peak areas were normalized for loading using a digital image of the
ethidium bromide-stained gel taken prior to electrophoretic transfer.
, TCM1; , CYH2; ,
pre-tRNALeu.
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The effect of tunicamycin was also examined for two RP mRNAs
(
TCM1 and
CYH2), actin mRNA (
ACT1),
and U3 snoRNA (Fig.
2). In
agreement with previous observations, RP
mRNA levels decreased
substantially in the presence of tunicamycin,
with little or no
change in the levels of actin mRNA or U3 snoRNA
during the time
course (
20,
22). Given the naturally short
half-life of RP
mRNAs in wild-type cells (<10 min at 37°C) and
evidence that RP
mRNA stability does not change with inhibition of the
secretory
pathway, the decrease in RP mRNA levels can be attributed
solely
to repression of their transcription (
17).
Quantitative analysis
of the Northern blots reveals virtually identical
kinetics for
the inhibition of the two RP mRNAs and the
tRNA
Leu precursor (Fig.
2B), suggesting that the
transcription of RP
and tRNA genes is coordinately repressed in
secretion-defective
cells and that a common signaling pathway may
mediate this
response.
Components of the cell integrity pathway are required for
repression of ribosome and tRNA synthesis.
Recent studies of the
regulatory circuit connecting the secretory pathway and ribosome
synthesis have revealed that transcriptional repression of rDNA and RP
genes is blocked in a PKC deletion (pkc1
) strain
(22). This finding, together with the ability of a
membrane-stretching agent, chlorpromazine, to repress RP genes,
suggested a role for the cell integrity pathway in signaling this
response (22). The cell integrity pathway mediates cell
cycle-regulated cell wall synthesis and responds to a variety of
environmental stimuli, including elevated temperature (37 to 39°C),
hypoosmotic shock, and pheromone treatment (8). To determine
whether this pathway might also signal transcriptional repression in
secretion-blocked cells, we first sought to extend the results obtained
with the PKC deletion to the Pol III system. Congenic strains
containing all combinations of the SEC1/sec1-1 and
PKC1/pkc1
genes were grown to mid-log phase at 23°C in
YPD containing 1 M sorbitol (sorbitol suppresses the cell lysis
phenotype of pkc1
strains but not the sec1-1
secretory defect [16, 22]). Analysis of lysine
precursor tRNAs after a shift to the nonpermissive temperature shows
that their levels decrease in the sec1-1 strain, reaching 20% of the level prior to the temperature shift after 90 min (Fig. 3A). However, in the sec1-1
pkc1
strain, the decrease was considerably less pronounced.
Indeed, lysine precursor tRNA levels in the double-mutant strain were
indistinguishable from those in the wild-type and pkc1
strains, declining only to about 60% of the level prior to the
temperature shift after 90 min. Similar results were obtained using a
leucine precursor tRNA probe. The results for these Pol III transcripts
parallel the findings for the large rRNAs and RP mRNAs in the same
strains (22). Together, these data suggest that PKC mediates
transcriptional repression of the protein-synthesizing machinery in
response to a defect in the secretory pathway.

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FIG. 3.
Deletion of Wsc proteins or PKC1 abrogates
repression of RP and tRNA genes due to a secretory defect. (A) Congenic
strains (MN51 through MN54, differing at the SEC1 and
PKC1 loci) were grown at 23°C in YPD plus 1 M sorbitol and
shifted to 37°C. RNAs (20 µg) from cells harvested before and at
various times after the temperature shift were analyzed by Northern
blotting using an intron-specific lysine tRNA probe. The plotted data
represent the sum of the areas determined by peak integration for both
intron-containing tRNALys precursors (see, e.g., Fig. 1A).
, PKC1 SEC1; , PKC1 sec1-1; ,
pkc1 SEC1; , pkc1 sec1-1. (B) Isogenic
strains (ALHWT, ALH715, and ALH718) differing at the WSC
loci were grown at 30°C in YPD plus 1 M sorbitol to mid-log phase
before the addition of tunicamycin. RNAs from cells harvested at the
indicated times were analyzed by Northern blotting using actin and RP
mRNA probes and the 5' flank pre-tRNALeu probe (as in Fig.
2A).
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The farthest-upstream components of the cell integrity pathway that
have been identified to date are the Wsc proteins. The
four Wsc
proteins and the related Mid2 gene product are putative
cell surface
sensors based on their localization, topology, and
glycosylation
(
7,
25,
28). Although the functions of the
Wsc proteins in
cell integrity signaling are partially redundant,
the phenotype of a
wsc1
mutation is more severe than that for
deletions of
the other family members and results in an osmotic
remedial cell lysis
phenotype at 37 to 39°C. We therefore examined
the effect of
tunicamycin on the transcription of RP and tRNA
genes in a set of
isogenic strains with deletions of
WSC1 and
either
WSC2 or
WSC3. As shown by the levels of RP mRNAs
and pre-tRNA
Leu, transcriptional repression of the
corresponding genes in strain
ALHWT was complete 2 h after the
addition of tunicamycin. This
indicates that strain ALHWT is somewhat
more sensitive to tunicamycin
than W303

(compare Fig.
2 and
3B).
However, for both the
wsc1
wsc2
and
wsc1
wsc3
strains, little or no decrease in the levels
of RP mRNAs
or precursor tRNA was seen up to 3 h after the addition
of the
drug (Fig.
3B). Thus, deletion of these Wsc proteins severely
impairs
transcriptional repression in secretion-blocked cells.
These results
demonstrate that the upstream components of the
cell integrity pathway,
specifically the Wsc proteins and PKC,
are part of a common signaling
pathway mediating transcriptional
repression of ribosome and tRNA
synthesis.
A novel signaling pathway downstream of PKC.
The cell
integrity pathway is the only PKC pathway that has been defined in
yeast (8). Signaling through this pathway involves PKC
activation of a specific downstream MAP kinase cascade comprising the
MEK kinase Bck1, a pair of redundant MEKs (Mkk1 and Mkk2), and the MAP
kinase Slt2 (Mpk1). Activation of Slt2 by the MEKs involves dual
phosphorylation at a unique ... TEY ... sequence in the
kinase domain. We therefore sought to confirm that Slt2 is activated in
cells with blocks in the secretory pathway by Western blotting using a
phosphospecific antibody. Wild-type and sly1-1 cells were
grown at 23°C to mid-log phase and then shifted to 33°C. This
temperature is nonpermissive for sly1-1 (20) and maintains a low background level of activated Slt2 in a wild-type strain (Fig. 4A). Cells collected at
various times (up to 90 min after the temperature shift) were lysed
under denaturing conditions, and equal amounts of the extracts were
analyzed by Western blotting (26). An increase in the amount
of doubly phosphorylated Slt2 was apparent in the mutant strain, but
not in the wild-type strain, after 60 and 90 min at the nonpermissive
temperature (Fig. 4A). Since activation of the cell integrity pathway
does not affect the steady-state level of Slt2 protein (8, 13,
28), we conclude that inhibition of the secretory pathway leads
to activation of the Slt2 kinase. In a parallel experiment, RNAs from
cells grown under the same conditions were analyzed by Northern
blotting using a leucine precursor tRNA-specific probe. This allowed a quantitative comparison of precursor tRNALeu synthesis in
the sly1-1 strain at 33 and 37°C (Fig. 4B) and a qualitative comparison of Pol III transcriptional repression and Slt2
activation (compare Fig. 4A with Fig. 4B). The data show that (i) the
kinetics of repression of the pre-Leu tRNA is slower, and the end point
reached is higher, in the sly1-1 strain grown at 33 versus
37°C and (ii) pre-Leu tRNA synthesis is fully repressed at times when
activated Slt2 is readily detected. An equivalent correlation between
the activation of Slt2 and the repression of RP and tRNA genes was
obtained with tunicamycin-treated wild-type cells (data not shown).
Although Slt2 is clearly activated in secretion-blocked cells, these
experiments do not address whether Slt2 activation is required for or
is coincident with transcriptional repression.

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FIG. 4.
Slt2 activation and Pol III transcriptional repression
in a sly1-1 strain. Wild-type (W303 ) and
sly1-1 (312) strains were grown at 23°C, shifted to
33°C, and harvested at various times to prepare total denaturing cell
lysates for Western blotting or RNA for Northern analysis. (A) A
Western blot was probed sequentially with a phosphospecific MAP kinase
antibody that recognizes activated yeast Slt2 (Slt2*) (28)
and antibodies to TBP, which provide a control for protein loading. The
panel at the upper left shows the signal for activated ERK1 (ERK1*)
and activated Slt2 (from an extract of 39°C heat-shocked yeast
cells). (B) Northern analysis of pre-tRNALeu levels in the
sly1-1 strain, shifted from 23 to 33°C ( ) or to 37°C
( ) and from a wild-type strain (W303 ) shifted from 23 to 37°C
( ). The data at 37°C were quantified from Fig. 1A.
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To test directly whether components of the cell integrity pathway MAP
kinase cascade are necessary for transcriptional repression
in response
to a secretory defect, we examined the effects of
tunicamycin on RP
mRNA and tRNA levels in a
bck1
strain and in
a strain
containing a catalytically inactive
SLT2 allele,
slt2 K54R (
36). Neither mutation in the MAP
kinase cascade affected
transcriptional repression of RP or tRNA genes
(Fig.
5). Quantitative
analysis of the
blots revealed the same kinetics of repression
for pre-Leu tRNA and
TCM1 mRNA in the mutant strains as for pre-Leu
tRNA in
isogenic wild-type strains (Fig.
5B and D) and in W303
(Fig.
2B).
Moreover, repression occurs without significant effects
on actin mRNA
(up to 180 min) or U3 snoRNA (Fig.
5) and without
changes in the
steady-state levels of the abundant small RNAs
(5.8S, 5S, or mature
tRNA [data not shown]). Since Slt2 is dependent
on PKC and downstream
components of the cell integrity pathway
for activation (
8),
and the known biochemical consequences
of activating the cell integrity
pathway (e.g., phosphorylation
of Swi6 and Rlm1) are dependent on Slt2
(
19,
31), our data
suggest that the cell integrity pathway
is bifurcated downstream
of PKC and that a novel effector branch of the
pathway mediates
transcriptional repression in secretion-blocked cells.

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FIG. 5.
Inactivation of the cell integrity pathway MAP kinase
cascade does not affect repression of RP or tRNA genes in response to
tunicamycin. (A) A strain with the MEK kinase BCK1 deleted
(DL252) and an isogenic control (1783) were grown at 25°C in YPD to
mid-log phase before the addition of tunicamycin. Cells were harvested
at various times thereafter to prepare RNA for Northern analysis. The
same probes were used as in Fig. 2A. (B) Quantitation of pre-Leu tRNA
and TCM1 mRNA from panel A (for details, see Materials and
Methods). (C) Strain YK193 (19), which contains a
catalytically inactive SLT2 allele (slt2 K54R
[36]), and its isogenic wild-type control (Y783WT)
were grown and analyzed as described for panel A except that SC-uracil
medium was used. (D) Quantitation of pre-Leu tRNA and TCM1
mRNA from panel C.
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rap1-17 affects a Pol II-specific branch of a signaling
pathway monitoring secretory function.
In previous work
(20), the repression of RP gene transcription resulting from
a defect in the secretory pathway was attenuated by a mutation in
RAP1 (rap1-17) that deletes its silencing domain. This effect was observed for RP genes that contain Rap1-binding sites
in their promoter (the vast majority) as well as for RP genes that do
not (20). These findings suggested that Rap1 represses the
transcription of RP genes without necessarily binding to their promoters. Although RAP1 is not known to play a role in Pol
III transcription, the preceding observations prompted us to test whether rap1-17 could prevent the repression of Pol III
transcription. Congenic strains with all combinations of the
RAP1/rap1-17 and SLY1/sly1-1 genes were grown at
23°C and then shifted to 36°C to obtain cells for RNA preparation
(20). Subsequent Northern analysis using a leucine precursor
tRNA-specific probe showed no effect of the rap1-17 mutation
on transcriptional repression by the sly1-1 secretory block
(Fig. 6). Leucine precursor tRNA synthesis decreased in both the sly1-1 RAP1 and sly1-1
rap1-17 strains, such that 90 min after the temperature shift, the
amount of pre-tRNALeu was only 20 to 25% of the level
prior to the shift. In contrast, the amount of pre-tRNALeu
in the SLY1 rap1-17 strain at this time was still greater
than 72% of that in the 23°C control. Surprisingly, the
rap1-17 mutation increased the level of leucine tRNA
precursors about threefold (at 23°C) compared to those in the
RAP1 strains, regardless of their secretory competence. This
result reveals a previously unknown negative effect of RAP1
on Pol III transcription. It is clear, however, that RAP1
does not mediate signaling to the Pol III transcription machinery in
response to the sly1-1 secretory defect. In light of results
obtained previously for RP gene transcription in these strains
(20, 22), the present findings indicate that the signaling pathway mediating the secretory defect is bifurcated downstream of PKC
to produce Pol II- and Pol III-specific effector branches (Fig.
7).

View larger version (40K):
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|
FIG. 6.
RAP1 does not mediate repression of Pol III
transcription in secretion-blocked cells. Congenic strains (KM011,
KM013, KM014, and KM016) containing all pairwise combinations of
SLY1 and sly1-1 with RAP1 and
rap1-17 were grown at 23°C and shifted to 36°C. RNA (20 µg) from cells harvested before and after the temperature shift was
analyzed by Northern blotting using the 5' flank
pre-tRNALeu probe. The quantified data are described in the
text.
|
|

View larger version (17K):
[in this window]
[in a new window]
|
FIG. 7.
Model of the secretory signaling pathway mediating
transcriptional repression of ribosome and tRNA synthesis. Turgor
pressure generated by ongoing protein synthesis and a reduction or
blockage in the delivery of secretory vesicles to the plasma membrane
is proposed to activate the pathway. The guanine nucleotide exchange
factor Rom2 and the Rho1 GTPase are possible upstream components of the
secretory signaling pathway (between Wsc and Pkc1) based on studies of
actin depolarization (5). The number of steps downstream of
Pkc1 is unknown. Arrows indicate activation; bars indicate
repression.
|
|
 |
DISCUSSION |
The energetic cost of producing the machinery for protein
synthesis.
The work reported here, together with earlier studies
(30), shows that interruption of the secretory pathway in
yeast leads to transcriptional repression of the large rRNAs by Pol I,
RP genes by Pol II, and 5S rRNA and tRNA genes by Pol III. Thus, all of
the components of the ribosome as well as its tRNA substrates are
subject to this repression. Repression of transcription under these
conditions is not genome-wide, however, as the levels of several
glycolytic mRNAs (PGK1, PYK1, and
ENO1) and actin mRNA (which have half-lives of less than 20 min [10]) do not decrease in secretion-defective cells
(17, 18, 20-22). Indeed, the levels of some mRNAs (e.g.,
KAR2) increase significantly as interruption of the
secretory pathway leads to activation of the unfolded protein response
pathway (Fig. 2) (14, 17, 20). In rapidly growing yeast,
about 60% of the total nuclear transcription is dedicated to Pol I
synthesis of the large rRNAs (30). Another 14% is carried out by Pol III in the synthesis of 5S rRNA and tRNAs (determined from
the pulse-labeling experiment [Fig. 2]). Of the remaining ~26% of
nuclear transcription that is directed by Pol II, around 50% of the
initiation events take place on RP genes (17, 30). Thus, we
estimate that more than 85% of the total nuclear transcription can be
repressed when the secretory pathway is blocked. Given the enormous
amount of metabolic energy consumed with this level of transcriptional
activity, it makes good biological sense for cells such as yeast to
shut down the production of ribosomes and ribosomal substrates when
they are unable to expand their plasma membranes. The conservation of
metabolic energy achieved by this repression may help to promote cell
survival under adverse conditions.
A branch of the cell integrity pathway mediates transcriptional
repression.
The four Wsc proteins and the related Mid2 protein are
thought to sense and signal changes in cell wall integrity resulting from heat stress, hypotonic stress, and pheromone treatment (25, 28). The Wsc proteins signal PKC either directly or indirectly (via Rom2 and Rho1 (5, 8). PKC in turn relays the signals from the Wsc proteins to the downstream MAP kinase cascade, ending in
the activation of Slt2, in order to induce the expression of cell wall
synthesis genes for remodeling or repair of the cell wall (8,
28). wsc1
and pkc1
mutants have an
osmotic remedial cell lysis phenotype at or above 25°C that is
characteristic of cell integrity pathway deletion mutants.
The results presented above demonstrate that
wsc1
and
pkc1
mutants are also defective in the repression of
ribosome and
tRNA synthesis when the secretory pathway is blocked (Fig.
3).
Further evidence for a role of the Wsc proteins and PKC in
signaling
a secretory defect is our finding that Slt2 is activated in
sly1-1 and tunicamycin-treated cells (Fig.
4A and data not
shown). Slt2
activation is tightly linked to the cell integrity pathway
(
8):
it is abolished in
pkc1
strains
(reference
13 and our unpublished
data) and is
largely, although not completely, defective in a
wsc1 strain
(residual activation in this case reflects the partially
redundant
function of the Wsc proteins) (
28). Thus, the initial
stages
of the response to a secretory defect or to cell wall stress
seem to be
the same. However, the response to a secretory defect
does not lead
primarily to the activation of transcription, but
to its repression,
specifically toward the transcription of genes
comprising the
protein-synthetic machinery. Moreover, components
of the cell integrity
pathway MAP kinase cascade (Bck1 and Slt2)
are not required for this
response (Fig.
5). These observations
suggest that the cell integrity
pathway is bifurcated downstream
of PKC and that a novel effector
branch of the pathway mediates
transcriptional repression (Fig.
7).
Bifurcation of the signaling
pathway downstream of PKC has been
suggested previously, based
on genetic studies (
6,
9).
However, the functions of the
novel pathway and its components have
remained obscure. We suggest
that this branch of the cell integrity
pathway is responsible
for the repression of genes that make up the
protein-synthesizing
machinery. Activation of this pathway frees
substantial resources
needed by a cell under stress and reduces the
increased stress
caused by ongoing protein synthesis under conditions
where the
cell is unable to synthesize either plasma membrane or cell
wall.
Independent evidence for a bifurcated signaling pathway below PKC has
come from the observation that the depolarization of
both actin and the
integral plasma membrane protein

-1,3-glucan
synthase upon heat
shock requires Wsc1 and Rom2 (the guanine nucleotide
exchange factor of
Rho1) and can be induced in strains expressing
hyperactivated (toxic)
alleles of
RHO1 and
PKC1 (
5). As in
our experiments,
BCK1 and
SLT2 are not required
for the depolarization
response. These findings raise the possibility
that a common PKC
effector pathway mediates both actin depolarization
and transcriptional
repression of ribosome synthesis. However, there
are differences
in the signaling of these responses: conditions which
cause actin
depolarization (e.g., incubation at 37°C for 35 min)
(
5) do
not result in PKC-dependent repression of ribosome or
tRNA synthesis
(Fig.
1) (
22). Thus, there may be three
functionally distinct
branches of the PKC pathway. In any event,
further branching of
the PKC effector pathway mediating transcriptional
repression
is required to enable signaling to the Pol I, the Pol II,
and
the Pol III transcription machinery (Fig.
7). This is indicated
by
the ability of a silencing defective allele of
RAP1
(
rap1-17)
to block repression of RP genes but not tRNA genes
(Fig.
6) or
rDNA (data not shown) upon inactivation of the secretory
pathway.
Implications for the coordination of ribosome and tRNA synthesis
with cell growth.
The finding that transcriptional repression in
secretion-defective cells requires members of the Wsc family of
putative plasma membrane sensors and continued protein synthesis
(21), together with the ability of a membrane stretch agent,
chlorpromazine, to induce repression of RP genes (22),
suggests that activation of the signaling pathway in secretion-blocked
cells is initiated by the elevated internal turgor pressure (Fig. 7).
Presumably, this condition is extreme in most of our experiments due to
the complete interruption of the secretory pathway. However, analysis of a sly1-1 mutant at 33 and 37°C shows that the kinetics
and magnitude of repression of a tRNA gene are clearly different (Fig. 4B). Similarly, secretory mutants that are variably leaky lead to
different levels of repression of rRNA and RP gene transcription (21). Thus, the severity of the secretion defect influences the level of transcriptional repression. It seems likely, therefore, that turgor pressure, and its effect on transcription, provides a means
for balancing the production of the protein-synthesizing machinery with
the delivery of secretory vesicles to the plasma membrane.
 |
ACKNOWLEDGMENTS |
We thank Roymarie Ballester, David Levin, and Mike Snyder for
providing yeast strains and Pierre-Alain Delley and Mike Hall for
communicating their results prior to publication.
This work was supported by NIH grants to I.M.W. (GM42728) and J.R.W.
(GM25532) and by an award from the Irma T. Hirschl Trust to I.M.W.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Department of
Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park
Ave., Bronx, NY 10461. Phone: (718) 430-2839. Fax: (718) 430-8565. E-mail: willis{at}aecom.yu.edu.
Present address: Department of Physiology and Cellular Biophysics,
College of Physicians and Surgeons, Columbia University, New York, NY 10032.
 |
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