Previous Article | Next Article 
Molecular and Cellular Biology, August 1999, p. 5393-5404, Vol. 19, No. 8
0270-7306/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.
Transcriptional Elements Involved in the Repression
of Ribosomal Protein Synthesis
Baojie
Li,
Concepcion R.
Nierras,
and
Jonathan R.
Warner*
Department of Cell Biology, Albert Einstein
College of Medicine, Bronx, New York 10461
Received 29 January 1999/Returned for modification 14 April
1999/Accepted 11 May 1999
 |
ABSTRACT |
The ribosomal proteins (RPs) of Saccharomyces
cerevisiae are encoded by 137 genes that are among the most
transcriptionally active in the genome. These genes are coordinately
regulated: a shift up in temperature leads to a rapid, but temporary,
decline in RP mRNA levels. A defect in any part of the secretory
pathway leads to greatly reduced ribosome synthesis, including the
rapid loss of RP mRNA. Here we demonstrate that the loss of RP mRNA is
due to the rapid transcriptional silencing of the RP genes, coupled to
the naturally short lifetime of their transcripts. The data suggest
further that a global inhibition of polymerase II transcription leads
to overestimates of the stability of individual mRNAs. The
transcription of most RP genes is activated by two Rap1p binding sites,
250 to 400 bp upstream from the initiation of transcription. Rap1p is
both an activator and a silencer of transcription. The swapping of
promoters between RPL30 and ACT1 or
GAL1 demonstrated that the Rap1p binding sites of
RPL30 are sufficient to silence the transcription of
ACT1 in response to a defect in the secretory pathway.
Sir3p and Sir4p, implicated in the Rap1p-mediated repression of silent
mating type genes and of telomere-proximal genes, do not influence such
silencing of RP genes. Sir2p, implicated in the silencing both of the
silent mating type genes and of genes within the ribosomal DNA locus, does not influence the repression of either RP or rRNA genes. Surprisingly, the 180-bp sequence of RPL30 that lies
between the Rap1p sites and the transcription initiation site is also
sufficient to silence the Gal4p-driven transcription in response to a
defect in the secretory pathway, by a mechanism that requires the
silencing region of Rap1p. We conclude that for Rap1p to activate the
transcription of an RP gene it must bind to upstream sequences; yet for
Rap1p to repress the transcription of an RP gene it need not bind to the gene directly. Thus, the cell has evolved a two-pronged approach to
effect the rapid extinction of RP synthesis in response to the stress
imposed by a heat shock or by a failure of the secretory pathway.
Calculations based on recent transcriptome data and on the half-life of
the RP mRNAs suggest that in a rapidly growing cell the transcription
of RP mRNAs accounts for nearly 50% of the total transcriptional
events initiated by RNA polymerase II. Thus, the sudden silencing of
the RP genes must have a dramatic effect on the overall transcriptional
economy of the cell.
| |
INTRODUCTION |
The Saccharomyces
cerevisiae cell invests enormous resources in the synthesis of
ribosomes. In a rapidly growing cell, the 100 or more rRNA genes are
responsible for at least 60% of total transcription (59).
The 137 ribosomal protein (RP) genes are among the most active in the
genome (57). As a result, the cell has evolved mechanisms
that tightly control the synthesis of the components of the ribosome.
The 78 RPs are synthesized in nearly equimolar amounts that are matched
to the synthesis of rRNA. Furthermore, the synthesis of these
components is coordinately responsive to many changes within or outside
the cell, including heat shock, carbon source, and nutrient
availability (reviewed in references 44 and
59).
The primary level of regulation is at transcription (7, 16,
24). Most RP genes have similar promoter motifs, consisting of
two Rap1p binding sites in tandem arrangement 250 to 400 bp upstream of
the transcription initiation site recently compiled by Lascaris et al.
(26), followed by one or two T-rich regions, and then a
region of about 180 bp that includes the putative TATA element. Serial
promoter deletions of RP genes, including RPS14A (CRY1), RPL25, and RPL28
(CYH2), have shown that the Rap1p sites are responsible for
about 90% of promoter activity, with the rest due to the T-rich
regions (41, 45, 47). Deletions downstream of the T-rich
elements have little effect on the rate of transcription but can affect
the initiation site (47). For a small minority of RP genes,
including RPL3, RPL4A, RPL4B, and
RPS28A, a single Abf1p site replaces the two Rap1p sites
(8, 13). Nevertheless, such genes appear to be regulated
coordinately with the others. (In this paper, we have used the new
nomenclature for RPs and their genes that was recently adopted
(32, 64a). Thus, L30 was previously known as L32, L3 was
previously known as Tcm1p, and L8 was previously known as L4.)
Rap1p is an essential, abundant DNA-binding protein that has several
functions in the cell. It is a context-dependent transcription regulator (50), responsible for activating the transcription of many of the most highly transcribed genes, encoding not only the RPs
and other translation factors but also the very abundant glycolytic
enzymes (reviewed in reference 49). Rap1p also acts as a transcriptional silencer in at least two contexts. At the silent
mating type loci, Rap1p cooperates with Abf1p and the origin of
replication complex (ORC) to repress transcription (1). At
the telomeres, Rap1p binds to the [C1-3A]n
repeats (63), leading to the silencing of genes adjacent to
telomeres. In both cases Rap1p recruits multiple copies of Sir3p and
Sir4p that participate in the silencing, perhaps by interacting with
the tails of histones H3 and H4 (38). A mutant allele,
rap1s, relieves the repression at silent mating
type loci. The overexpression of Sir3p or Sir4p can restore the
repression (53).
When yeast cells growing at 23°C are shifted to 37°C, both growth
and protein synthesis continue unabated; indeed, depending on strain
background, they sometimes increase (11). Furthermore, mRNA
synthesis, measured by the incorporation of [3H]uracil
into poly(A)+ RNA, is unaffected (24). Yet,
during the first 20 min after such a shift the level of RP mRNAs
declines by about 80% and then recovers to the original level by about
60 min (11, 15). This down-regulation of RP mRNA has been
attributed to a temporary transcriptional silencing of RP genes
(24) and to an increased turnover of RP mRNAs
(15). In neither case have the elements responsible been
identified (15, 45).
Recently, we have shown that a defect at any of several points in the
secretory pathway down-regulates the synthesis of ribosomes, through
the repression of transcription of both rRNA and RP genes (28,
36). Inhibitors that disrupt the secretory pathway, such as
brefeldin A and tunicamycin, also repress ribosome synthesis. A similar
effect on rRNA transcription was observed in a sec23 mutant
(29). These results suggest that there exists an
intracellular signal transduction pathway between the secretory
apparatus and the master control of ribosome biosynthesis.
To identify the elements of an RP gene that makes it subject to
repression by a temperature shock and by the failure of the secretory
pathway, we have carried out experiments which demonstrate (i) that the
rapid decline in mRNA levels is due entirely to the rapid repression of
transcription, coupled to a normal, rapid turnover of the mRNA (this
repression does not depend on the presence of Sir2p, Sir3p, or Sir4p)
and (ii) that the repression of transcription is mediated by two
cis elements, the Rap1p binding sites and a 180-bp sequence
just upstream of the transcription initiation site. Either of these
elements alone can mediate at least 75% of repression.
| |
MATERIALS AND METHODS |
Strains.
The strains used in this study are listed in Table
1. Unless otherwise stated, cultures were
grown on 2% yeast extract-1% Bacto Peptone-2% glucose (YPD) at
23°C. Cultures were shifted from 23 to 37°C by pouring them into a
large, prewarmed flask shaking in a water bath. Cultures were shifted
from YPGal to YPD by filtration onto a Millipore filter which was
immediately transferred to the new medium. The whole operation took
less than 20 s.
Yeast total RNA isolation.
Generally, 10-ml volumes of
cultures in log phase were harvested by pouring them on crushed ice
(46). Cells were collected by centrifugation, resuspended in
400 µl of AE buffer (50 mM NaAc [pH 5.3], 1 mM EDTA), and
transferred to microcentrifuge tubes. Forty microliters of 10% sodium
dodecyl sulfate was added, and the mixture was vortexed. An equal
volume of fresh, AE buffer-saturated phenol was added, and the mixture
was vortexed for 2 min. The samples were then incubated at 65°C for 4 min and chilled rapidly in dry ice-ethanol until phenol crystals
appeared. The samples were centrifuged at maximum speed for 10 min, and
the aqueous layer was transferred to another tube, extracted with
phenol-chloroform at room temperature for 5 min, and then centrifuged
for 5 min. Total RNA was precipitated with ethanol, washed with 70%
ethanol, dried, and resuspended in 50 µl of sterile water.
RNA gel and Northern analysis.
Ten micrograms of total RNA
was fractionated on 1.5% agarose gels containing 6% formaldehyde. The
RNA was transferred to Nytran (Schleicher & Schuell) nylon membranes,
cross-linked with UV light, and then baked in a vacuum for 1 h at
80°C. Northern blot analysis was performed as described previously
(10). 32P-labelled antisense RNA probes and
oligodeoxynucleotides were used to detect mRNAs (36). rRNA
was labelled with [C3H3]methionine
(60) and analyzed by fluorography (36).
Construction of fused genes with site-directed mutagenesis.
For the ACT1 gene constructs, the A of ATG in the coding
region is at position +1. For RPL30, the transcription
initiation site is considered position +1 and is 58 nucleotides
upstream of ATG. To fuse the RPL30 promoter to the
ACT1 transcription unit, the URA3 gene was first
cloned into pMDJ8, which contains a 1.8-kb fragment with the complete
RPL30 sequence, from 
443 to +1520. The new plasmid,
containing divergently expressed URA3 and RPL30 genes, each from its own promoter, was then used as a template for PCR.
The left-hand primer contained ACT1 sequences from 410 to
364 and the reverse complement of URA3 sequences from +915 to +890. (The URA3 open reading frame [ORF] is 803 bp).
The right-hand primer contained ACT1 sequences from 96 to
141 and RPL30 sequences from 1 to 26. PCR amplified a
fragment in which the entire URA3 gene and RPL30
promoter sequences (to the transcription start site at +1) were
bracketed by ACT1 sequences. The PCR fragment was integrated
into the chromosomal ACT1 locus of strain 169ts or JW142 by
homologous recombination, selecting for URA3. The integration reconstituted the ACT1 transcription unit, under
the control of the RPL30 promoter (Fig. 4B). The correct
integration was verified by PCR. The correct initiation of
transcription was verified by primer extension. The resulting strain
was designated JW1201 (Table 1).
Constructs A to D (Fig.
4C) were made starting with a pUC19-based
plasmid carrying a 2.2-kb
EcoRI fragment from
RPL30. The
promoter region was replaced with a fragment
containing the promoter
of
ACT1 (construct A; Fig.
4B). From
this construct, the upstream
activating sequence (UAS) of
ACT1 was replaced with portions of
the UAS of
RPL30 (constructs B, C, and D; Fig.
4C). For use in
yeast,
the constructs were subcloned into the
CEN/URA3 plasmid,
pRS316 (
51). Primer extension revealed that about 50% of
the
transcripts initiated at the normal site for RPL32, and 50%
initiated
nine nucleotides
downstream.
Constructs E to H (Fig.
9A) were made, starting with the vector pRS316
carrying
RPL30. A large portion of the ORF downstream
of the
intron was replaced by the ORF encoding the green fluorescent
protein
(GFP), generating construct E (see text for details).
From construct E,
different portions of the
RPL30 promoter were
replaced with
a 500-bp fragment containing the four Gal4p binding
sites from
GAL1 (nucleotides
829 to
324; with the start codon
numbered +1), generating constructs F to
H.
Deletion mutations were constructed by PCR (
18). A circular
plasmid carrying the gene of interest was used as a template
for PCR
catalyzed by Tli DNA polymerase (Promega), which has proofreading
ability. PCR products were purified from an agarose gel with a
DNA
extraction kit (Qiagen). The purified DNA was used directly
for
self-ligation with the standard protocol, except that 10 U
of
polynucleotide kinase was included in the ligation reaction.
The
deletion constructs were
sequenced.
mRNA half-life measurement.
The strains to be tested were
grown overnight at 23°C to log phase. Cell cultures were concentrated
fivefold and then shifted to 37°C (43). At the indicated
time points 2-ml aliquots of the cultures were quickly collected and
frozen in dry ice-ethanol. Total RNA was isolated and analyzed as
described above. RNA levels were quantified relative to the U3
internal loading standard by using PhosphorImager (Molecular
Dynamics) analysis.
| |
RESULTS |
Repression of RP gene expression.
The mRNAs encoding RPs
appear to be particularly sensitive to environmental changes. As shown
in Fig. 1, a temperature shift from 23 to
37°C leads to a rapid decline in RP mRNA levels that is temporary in
wild-type (wt) cells (lanes 1 to 6) but permanent in cells with a
temperature-sensitive (ts) mutation in the secretory pathway,
exemplified by ypt6-1 (lanes 7 to 13). This is not true of
most non-RP genes, e.g., ACT1, or of the stable small
nucleolar RNA (snoRNA) U3. These results could be explained by the
hypothesis that the transcription of RP genes is extinguished after the
temperature shift, temporarily in wt cells and permanently in cells
with a defect in the secretory pathway. However, it has also been
suggested that the loss of RP mRNA after a heat shock is due instead to an accelerated turnover of RP mRNA (15).
View larger version (54K):
[in this window]
[in a new window]
|
FIG. 1.
The level of RP mRNAs is down-regulated in W303 (wild
type), 169ts (ypt6-1), and Y260 (rpb1-1) strains.
The indicated strains (Table 1) were grown to log phase in YPD at
23°C. An aliquot was harvested, the rest of the culture was shifted
to 37°C, and aliquots were harvested as indicated. Total RNA was
isolated, and 10 µg of RNA was analyzed by Northern blotting.
Individual RNAs were detected by using either antisense RNA probes, for
RPL30 and ACT1, or oligonucleotide probes, for
RPL3, RPL8, and U3 snoRNA, as described in
Materials and Methods.
|
|
In an attempt to distinguish between these alternatives we have
determined the half-life (
t1/2) of an RP mRNA
when its transcription
is halted in two distinct ways. In one case we
employed strain
Y260, which carries
rpb1-1, a ts allele of
the largest subunit
of RNA polymerase II (Pol II); in such cells, RNA
Pol II-dependent
transcription is reduced to less than 10% within 2 min after a
shift to 37°C (
42,
43). When Y260 is
transferred to the nonpermissive
temperature, the mRNA derived from
most RP genes declines with
a
t1/2 of about 20 min (Fig.
1, lanes 14 to 20; Fig.
2;
Table
2). The contrast between the
effects of a secretory mutant (Fig.
1, lanes 7 to 13) and a polymerase
mutant (lanes 14 to 20) (Fig.
2) supports the hypothesis that the
turnover of RP mRNAs is accelerated
due to heat shock in wt or
sec cells.
View larger version (19K):
[in this window]
[in a new window]
|
FIG. 2.
A portion of the data used to generate Table 2. Cultures
were handled as described in the text. The values represent the levels
of the indicated RNA measured by PhosphorImager analysis, normalized to
the amount of U3 RNA in that lane of the gel, and further normalized to
100% at the start of the experiment. Note that the repression of the
GAL1-L30 transcripts by glucose is indistinguishable from
the repression of the RPL30 transcripts by the secretory
defect. The transcripts shown are as follows, with the method of
repression in parentheses: ACT1-L30 (rpb1-1) ( ), RPL30
(rpb1-1) ( ), RPL30 (ypt6-1) ( ), GAL1-L30
(glucose) ( ), ACT1 (rpb1-1) ( ), RPL30-ACT1
(rpb1-1) ( ), and RPL30-ACT1 (ypt6-1) ( ).
|
|
To halt transcription in a way that does not depend on a temperature
shift we employed modified
RPL30 in which the UAS was
replaced with that of
GAL1. When this gene is used as the
sole
source of L30, cells will grow only in the presence of galactose.
In that case substantial
RPL30 mRNA is present (Fig.
3A). Once
the galactose is replaced with
glucose, transcription is immediately
repressed (
20,
30);
the mRNA derived both from
GAL1-RPL30 (Fig.
2) and from the
GAL1 and
GAL10 genes themselves declines
rapidly
(Fig.
3A), with a
t1/2 of 5 to 7 min for the
transcript
encoding L30 and 3 to 5 min for the
GAL genes
(Fig.
3A and Table
2), as observed previously (
3).
ACT1 mRNA and U3 RNA are unaffected.
This result suggests
that the
t1/2 for the
RPL30 mRNA is
artificially
extended in the
rpb1-1 strain. Indeed, when the
rpb1-1 strain
is grown on galactose and shifted to the
nonpermissive temperature,
the
t1/2 of the
GAL1 and
GAL10 mRNAs is increased greatly,
independent
of whether the galactose has been replaced with glucose
(Fig.
3B). Thus, the influence of
rpb1-1 on the measured
t1/2 of mRNAs
is not limited to the transcripts
of the RP genes.
View larger version (30K):
[in this window]
[in a new window]
|
FIG. 3.
(A) Direct measurement of the
t1/2 of the mRNA encoding L30. Strain JV7-2a
(rpl30 ::HIS3 [pYE: CEN, URA3
GAL1-RPL30]) was grown at 37°C in YPGal medium and shifted to
YPD (4% dextrose) as described in Materials and Methods. Cells were
harvested just before and at intervals after the shift, and RNA was
prepared and analyzed by Northern blotting as described previously.
After PhosphorImager analysis, the t1/2 of the
GAL1, GAL10, and GAL-RPL30 mRNAs was
determined by using the stable U3 RNA as a loading control (Table 2).
Note that the same experiment was carried out at 23°C, in which case
the t1/2 of the mRNAs was about twice as long.
(B) Extended t1/2 of the GAL1 and
GAL10 mRNAs in an rpb1-1 strain. Strain Y260
(rpb1-1) was grown in YPGal medium at 23°C. At zero time,
one sample was taken; half the remaining culture was shifted to 37°C,
and the other half was filtered and resuspended in YPD (4% dextrose),
prewarmed, and maintained at 37°C. Samples were taken at the
indicated times, and RNA was prepared and analyzed as for panel A.
|
|
Integrating the data of Fig.
1,
2, and
3 and Table
2 suggests the
following scenario. A temperature shift from 23 to 37°C
leads to an
immediate, but temporary, repression of the transcription
of RP genes.
In wt cells, the transcription of RP genes resumes
after about 20 min.
In a
sec mutant, however, the transcription
of RP genes does
not resume, and RP mRNA is reduced to a very
low level. These are
likely to be two separate phenomena because
either the ablation of the
protein kinase C pathway (
40) or
mutation of the silencing
domain of Rap1p (
35) relieves the
repression of
transcription due to a secretory defect without
affecting the
repression due to heat shock. The immediate kinetics
of the repression
due to a defect in the secretory pathway are
obscured by the cell's
response to heat shock. Nevertheless, we
have found that the inhibition
of the endoplasmic reticulum-Golgi
communication with brefeldin A
appears to repress the transcription
of RP genes within 15 min
(
36), while direct stress on the plasma
membrane, with the
intercalating drug chlorpromazine, leads to
repression almost
immediately (
40).
These data suggest that there is no need to invoke accelerated turnover
(
15) to explain the response of RP mRNA to a temperature
shift. The
t1/2 of RP mRNAs observed in response
to a temperature
shift in either a wt or a
sec cell is the
same as that observed
at 37°C when transcription is halted due to
glucose repression
of the
GAL1 promoter (Fig.
3A). However,
the extended
t1/2 of
both the RP and the GAL
mRNAs when transcription is extinguished
by the inactivation of RNA
polymerase II suggests that this experimental
approach may be having
broader physiological effects on the RNA
metabolism of the
cell.
RP promoter mediates repression.
The experiments whose results
are shown in Fig. 1 and 2 demonstrate an almost instantaneous and
complete repression of RP gene transcription. What sequence elements of
the RP genes are responsible for this repression? The promoter of
RPL30 (Fig. 4A) resembles the
promoters of most RP genes, with two Rap1p binding sites as the major
UAS, and one or two T-rich regions which have some promoter activity
(41, 45, 47), followed by a less well defined region that
contains the putative TATA box. Previous work has implicated the Rap1p
binding sites as the elements mediating the regulation of
transcription, in the response to a carbon source shift (7,
16), to amino acid starvation (37), and to cyclic AMP
(cAMP) (25, 39), but not in the response to a temperature shift (41, 45).
View larger version (30K):
[in this window]
[in a new window]
|
FIG. 4.
(A) The promoter of RPL30. The start codon is
boxed. The two Rap1p binding sites are indicated by a heavy underline,
and the two T-rich regions are indicated by a light underline. The
initiation of transcription, termed +1 and marked with an arrow, is 58 nucleotides upstream of ATG. (B) The RPL30-ACT1 fusion gene.
See Materials and Methods for details. (C) Constructing the fused gene
with the ACT1 promoter driving the RPL30
transcript (constructs A to D); see Materials and Methods. The stippled
area represents sequences from ACT1. Nucleotides from the
RPL30 promoter were fused to the ACT1 TATA region
to form constructs B, C, and D. The hatched boxes are ACT1
sequences; the open boxes are RPL30 sequences; the black
boxes represent the RPL30 Rap1p binding sites. The line
represents the L30 transcript. The nucleotide boundaries of the
RPL30 sequences are shown above the constructs, and those of
the ACT1 sequences are shown below the constructs. Because
the ACT1 gene has multiple sites of transcription
initiation, the numbering is in reference to ATG of the coding
region.
|
|
To determine which of the elements in the promoter of RP genes mediate
the repression of transcription in response to a defect
in the
secretory pathway we made two promoter swap constructs,
in which the
RPL30 promoter drives the
ACT1 transcript (Fig.
4B)
and the
ACT1 promoter drives the
RPL30
transcript (Fig.
4C). Primer
extension demonstrated that the resulting
ACT1 transcripts were
initiated at the same site as that for
the endogenous
ACT1; about
half of the
RPL30
transcripts were initiated at the correct site,
with the rest being
initiated nine nucleotides downstream (data
not shown). The
ACT1-RPL30 construct is not responsive to the
ypt6-1 mutation (Fig.
5, lanes
1 to 5). The
RPL30-ACT1 construct
is responsive to the
ypt6-1 mutation, with the level of its transcript
decreasing
monotonically from the time of the temperature shift
(Fig.
5, lanes 18 to 23, and Fig.
2). The rate of decline in
RPL30-ACT1 mRNA
is lower than that of
RPL30, with a
t1/2 of about 16 min,
presumably because the
intrinsic stability of the
ACT1 transcript
is greater. Once
again, the
t1/2 measured here is substantially
shorter than that measured with the
rpb1-1 mutation (Fig.
2
and
Table
2), reinforcing the suggestion that
rpb1-1 has a
broad
effect on mRNA stability.
View larger version (27K):
[in this window]
[in a new window]
|
FIG. 5.
Rap1p binding sites mediate the repression of RP mRNAs.
ypt6-1 rpl30::HIS3 strains
containing constructs A to D (strains BL174 to BL177; Table 1) and
strain JW1201, in which RPL30-ACT1 is the only source of
actin sequences, were grown to log phase at 23°C and then shifted to
37°C. Aliquots were harvested at the indicated times, and RNA was
prepared and analyzed as described previously.
|
|
Rap1p binding sites mediate RP gene repression.
If the
RPL30-ACT1 construct is repressed while the
ACT1-RPL30 transcript is not, the influence of the secretory
pathway on RPL30 must depend solely on sequences upstream of
the transcription initiation site. In an attempt to identify which
sequences are involved, the UAS of the ACT1 promoter of
construct A was replaced with fragments of the RPL30
promoter (constructs B, C, and D shown in Fig. 4C). Plasmids carrying
these genes were used to transform BL17, a diploid strain with the
genotype RPL30/rpl30::HIS3
YPT6/ypt6-1. Following sporulation and dissection of tetrads,
strains carrying ypt6-1 and with constructs A to D as the
only source of L30 were identified (strains BL174 to BL177 in Table 1).
At the permissive temperature, the level of mRNA derived from each of
the constructs was about the same (Fig.
5, zero time),
suggesting that
the two Rap1p sites (construct D) are sufficient
to substitute for the
UAS of
ACT1. Upon a shift to the nonpermissive
temperature,
there is a rapid decline in the levels of mRNA derived
from
constructs B, C, and D. Clearly the presence of Rap1p binding
sites,
either with (construct B) or without (construct D) T-rich
regions,
makes the test gene responsive to the secretion defect.
These results
suggest that in this context the 40-bp sequence
containing the two
Rap1p binding sites is a sufficient
cis element
to effect
repression in response to a defect in the secretory
pathway.
It has been reported that Rap1p is degraded in cells depleted of cAMP
(
39), resulting in the reduced transcription of RP
genes. To
determine if limiting Rap1p lies behind the repression
of RP
transcription in response to a defect in the secretory pathway,
we
overexpressed Rap1p in both W303 and 169ts, by transforming
each strain
with a 2µm plasmid carrying wt
RAP1. The shift of
the
transformants from 23 to 37°C led to a loss of RP mRNA that
was
indistinguishable from that shown in Fig.
1 and
5 (data not
shown),
suggesting that the repression of RP gene transcription
is not due to
limiting
Rap1p.
The SIR complex is not involved in the repression induced by
secretion defects.
While Rap1p is a major transcriptional
activator, it is also a major transcriptional silencer, at the silent
mating type loci and at telomeric regions (reviewed in reference
49). In both cases, Rap1p recruits Sir3p and Sir4p
to form a complex that inhibits the transcription of the adjacent genes
(38). Since our results implicate Rap1p in mediating the
repression of RP gene transcription, we asked if Sir3p and Sir4p are
involved in the repression. The effects of tunicamycin on the mRNA
levels of RP genes and others were determined in strains lacking
components of the SIR complex (Fig. 6).
It is apparent that the presence of tunicamycin leads to a substantial
repression of the transcripts of both RPS6 and RPL30, with little effect on ACT1 or
PYK1. The deletion of SIR2, SIR3, or
SIR4 does not alter the repression of the RP genes. The induction of KAR2 is an expression of the "unfolded
protein response" demonstrating that the tunicamycin is active on
these cells (4).
View larger version (99K):
[in this window]
[in a new window]
|
FIG. 6.
The SIR complex does not mediate the repression of RP
genes in response to a defect in the secretory pathway. Cultures of
strains YDS2 (wt), YDS714 (sir2), YDS430
(sir3), and YDV122 (sir4) were grown in YPD
at 30°C. One half of each culture was treated with 1 µg of
tunicamycin per ml for 2 h. All eight cultures were harvested on
crushed ice, and RNA was prepared and subjected to Northern analysis,
by using several probes.
|
|
As a more direct test, strains containing null alleles of either
SIR3 (YDS430) or
SIR4 (YDV122) were crossed with
169ts, the
strain carrying
ypt6-1. From each diploid, we
selected a tetrad
that provided the four combinations of the
YPT6 and
SIR3 alleles
(strains BL180 to BL183;
Table
1) or the
SIR4 allele (strains
BL185 to BL188; Table
1). If either Sir3p or Sir4p were essential
for the repression, its
absence would eliminate the repression
of RP mRNAs in cells carrying
the
ypt6-1 allele. As shown in Fig.
7, the repression of the transcription of
RP genes, induced either
in
YPT6 cells by heat shock or in
ypt6-1 cells by a failure in
the secretory pathway, depends
neither on Sir3p nor on Sir4p.
View larger version (63K):
[in this window]
[in a new window]
|
FIG. 7.
Neither Sir3p (A) nor Sir4p (B) is involved in the
repression of RP gene transcription in a sec mutant or
during heat shock. Strains of the indicated genotypes (Table 1) were
grown to log phase in YPD at 23°C. An aliquot was harvested, the
cultures were shifted to 37°C, and aliquots were harvested at the
indicated times. RNA was prepared and analyzed as described previously,
except that all RNAs were detected with 32P-labelled
oligonucleotide probes.
|
|
Sir2p is not necessary for repression of either rRNA or RP
genes.
Sir2p is another participant in the repression of the
silent mating type loci, although its relationship to Rap1p is less clear than that of Sir3p and Sir4p. Surprisingly, Sir2p has recently been shown to participate in the silencing of a Pol II-transcribed gene
within the ribosomal DNA locus (52), although it has not been implicated directly in the control of rRNA transcription. To
determine whether Sir2p plays a role in the repression of ribosome synthesis, we deleted SIR2 or its close relative
HST1, which can partially substitute for SIR2 in
silencing (5), from a strain carrying a ts mutation in
sly1, an essential component of the secretory pathway
(36), yielding strains JW1210 and JW1211. The results of
shifting these two strains to the nonpermissive temperature are shown
in Fig. 8. In this case, the cells were grown in a medium lacking methionine and pulsed for 3 min with [C3H3]methionine as a measure of rRNA
transcription. RNA prepared from the cells was separated on an
acrylamide gel, the upper portion was subjected to fluorography, and
the lower portion was subjected to Northern analysis. From the latter
it is apparent that the mRNA for L30 disappears rapidly, just as in the
ypt6-1 strain shown in Fig. 1. C3H3
groups are incorporated predominantly into 35S rRNA, which is then
processed through the intermediate 27S and 20S species to the mature
25S and 18S rRNAs (56). In a 3-min pulse (Fig. 8, 0-min
lanes), most of the radioactivity has already passed into the 27S and
20S intermediates, and some is in mature 18S rRNA. We have previously
shown that the transfer to the nonpermissive temperature causes a rapid
repression of rRNA transcription in sly1-1 cells, with
little effect on wt cells (36). Similarly, the transfer of
the sly1-1 sir2 or the sly1-1
hst1 double mutant strains to the nonpermissive
temperature leads to a strong inhibition of the incorporation of
C3H3 into rRNA (Fig. 8, 20- and 60-min lanes),
just as for the cells carrying sly1-1 alone. What little 35S
RNA is formed is processed slowly if at all, presumably due to a lack
of RPs. We conclude that neither Sir2p nor Hst1p is involved in the
repression of ribosome synthesis in response to a defect in the
secretory pathway.
View larger version (97K):
[in this window]
[in a new window]
|
FIG. 8.
Neither Sir2p nor Hst1p is involved in the repression of
ribosome synthesis in response to a defect in the secretory pathway.
Cultures of strains JW1210 and JW1211 were grown in methionine-free
dropout medium at the permissive temperature of 23°C. At zero time an
aliquot was labelled with 60 µCi
[C3H3]-methionine for three minutes and
poured onto crushed ice. The remainder of the culture was shifted to
37°C, and aliquots were similarly pulsed with
[C3H3]-methionine after 20 and 60 min. RNA
was prepared, and equal amounts were subjected to polyacrylamide gel
electrophoresis. The upper portion of the gel was impregnated with
En3Hance and subjected to fluorography to show the
incorporation of C3H3 groups into rRNA. The
lower portion was used for Northern analysis with probes against
RPL30 and against 5.8S rRNA as a loading control (5.8S rRNA
has no methyl groups).
|
|
Non-Rap1p binding sites also mediate RP gene repression.
Although Rap1p binding sites contribute most of the transcriptional
activation of RP genes, some activity remains after the deletion of the
Rap1p binding site, due to the T-rich elements (41, 45, 47).
This residual activity of the RP genes still responds to heat shock,
implicating sequences other than the Rap1p sites in the regulation of
transcription of these genes. To identify such sequences and to
determine if they are also involved in the response to a secretion
defect, we developed a series of constructs based on the reporter gene
RPL30-GFP, in which the ORF of GFP replaced the ORF of L30,
starting with amino acid 4 in the second exon of RPL30 (Fig.
9A, construct E). The spliced transcripts contain the 5' untranslated region of RPL30, seven
nucleotides from the RPL30 ORF, the GFP ORF, and the 3'
untranslated region of RPL30. Note that the repression of
RPL30 is independent of sequences downstream of the
transcription initiation site (ACT-RPL30; Fig. 5, lanes 1 to
5). Increasing portions of the RPL30 promoter were replaced
with four Gal4p binding sites derived from the GAL1 promoter, generating constructs F, G, and H (Fig. 9A). The reporter gene constructs, on CEN-based plasmids, were transformed
into cells carrying the ypt6-1 allele. The necessary L30
protein is supplied by the genomic RPL30. Since the GFP ORF
is 400 nucleotides longer, the RPL30 and
RPL30-GFP mRNAs can be compared directly on Northern blots
by using a probe complementary to the first exon of RPL30.
View larger version (42K):
[in this window]
[in a new window]
|
FIG. 9.
(A) Construction of fused genes between GAL1
and RPL30-GFP (constructs E to H). The stippled area
represents sequences from the GAL1 UAS. The nucleotide
boundaries of the RPL30 sequences are shown, and numbering
follows the conventions described in the legend to Fig. 3A. The black
boxes represent the RPL30 Rap1p binding sites. (B) The
180-bp cis element mediates the repression of RP gene
transcription in a sec mutant. ypt6-1 cells
carrying constructs E to H were grown to log phase in uracil-free
medium containing 2% glucose at 23°C. An aliquot was harvested, the
rest of the cultures were shifted to 37°C, and aliquots were
harvested at intervals. Total RNA was isolated and analyzed as
described previously. mRNAs for RPL30 and
RPL30-GFP were detected with an RNA probe that is
complementary to the first exon of RPL30. The snoRNA U3 was
detected with an oligonucleotide probe. (C) The same as panel B except
that cells were grown in 2% galactose to induce the GAL1
UAS. GAL1 mRNA was detected with an antisense RNA probe.
|
|
For the first set of experiments the cells were grown in glucose to
repress transcription from the
GAL1 region, thereby
revealing
the transcriptional contribution of the residual
RPL30 sequences
(Fig.
9B). In a
ypt6-1
background, following a temperature shift,
construct E
(
RPL30-GFP) is repressed as severely as endogenous
RPL30, confirming that the promoter of the RP genes mediates
the
repression caused by a failure in the secretory pathway. Deletion
of the two Rap1p binding sites, leaving the T-rich domains (construct
F), leads to the loss of 90% of the transcriptional activity.
The 10%
of the activity remaining is repressed as severely as
endogenous
RPL30. The presence of a single T-rich domain (construct
G)
has only 5% of normal transcription, also repressible. Deletion
of
both Rap1 sites and both T-rich domains (construct H) leads
to a loss
of any detectable transcription. These results confirm
that the T-rich
region can activate some transcription of
RPL30,
consistent
with the observations for the other RP genes
RPL28,
RPS14, and
RPL25 (
41,
45,
47).
Nevertheless, upon a temperature
shift whatever residual transcription
that remains is repressed
in the
ypt6-1 mutant (Fig.
9B).
This result, in the absence of
Rap1p sites, implicates the remaining
downstream elements of the
RPL30 promoter in the repression
of
transcription.
Growth of these strains in a medium containing galactose permits Gal4p
binding to the sites present in constructs F, G, and
H, activating
transcription, at the permissive temperature, to
slightly higher levels
than with the
RPL30 promoter itself (constructs
F, G, and H;
Fig.
9C). Nevertheless, when the cells are shifted
from 23 to 37°C,
the transcription of constructs F, G, and H is
strongly repressed. The
level of
GAL1 transcripts is not dramatically
affected, at
least at 20 and 40 min after the temperature shift
(Fig.
9C). Since the
t1/2 of
GAL1 transcripts is <5 min
(
3)
(Fig.
3A), Gal4p-promoted transcription must be
continuing. Comparison
of construct E with constructs F, G, and H
suggests that a defect
in the secretory pathway can largely, though not
completely, repress
the transcription of an RP gene that is driven by a
novel activator,
in this case Gal4p. As the results for constructs F
and H barely
differ, we again conclude that the T-rich regions play
little
role in the repression of transcription. Thus, the repression
of
construct H suggests that the 180 bp that lie between the T-rich
elements and the origin of transcription of
RPL30 contain
sequence
elements that are sufficient for a major proportion of the
sec-dependent
repression of transcription of an RP gene.
Comparing the data
from Fig.
5 and
9 leads us to conclude that either
the Rap1p sites
or the 180-bp region will respond to the repression
effected by
a failure in the secretory pathway. In a different context,
Neuman-Silberberg
et al. (
39) also concluded that
Rap1p-binding sites and downstream
sequences could play separate roles
in the regulation of RP
transcription.
Is TAF145 responsible for the repression of RP gene
transcription?
A recent report suggests that the transcription of
many of the RP genes is particularly vulnerable to a mutation in the
transcription factor TAFII145 (48). Perhaps
TAFII145 is responsible for the effects of the
180-nucleotide region implicated by construct H (Fig. 9B), since this
region contains the TATA box with which TAFII145 is
presumably associated. However, while both IPP1
(48) and ACT1 (our unpublished data) are severely
repressed by ts mutants of TAFII145, they are not repressed
by a ts mutant in the secretory pathway (IPP1; data not
shown). Finally, a genome-wide analysis of the transcriptional effects
of a ts allele of TAFII145 suggests little specificity for
RP genes (17). Thus, it appears that TAFII145 is
not the agent responsible for the repression of transcription of the RP
genes under these conditions.
| |
DISCUSSION |
Turnover of RP mRNA.
The determination of the intrinsic
t1/2 of an mRNA presents several experimental
uncertainties. The most direct but most demanding method is the
approach to equilibrium, which requires not only sensitive
hybridization methods but also the determination of the approach to
equilibrium of the nucleotide pools (12, 23). Alternate
methods require turning off the transcription of all mRNA, using either
inhibitors or the ts allele of rpb1 (reviewed in reference
2). The former have proved inconsistent in yeast. The latter involves three perturbations of the cell: the raising of the
temperature, which brings the heat shock response into play, the
inhibition of any mRNA that might play a direct role in the
t1/2 of a specific mRNA, and the gradual loss of
all the cell's mRNAs, which can change the dynamic of translation and, consequently, of turnover. A more specific approach is the use of a
repressible promoter, such as GAL1, with which one can turn off the expression of a limited number of genes.
It is clear from Fig.
1,
2, and
3, as well as from Table
2, that the
decline of RP mRNA after a temperature shift, in either
wt or
sec cells, is similar to that observed when the RP mRNA
is
under the control of the
GAL1 promoter that is suddenly
repressed.
This result has two major implications. It suggests that a
heat
shock temporarily represses and a
sec mutant
permanently represses
RP transcription to nearly the same degree as
glucose does the
Gal4p-driven genes. It also suggests that the
intrinsic
t1/2 of
RP mRNAs can be estimated from
the decline of the mRNA after a
heat shock; for most RP mRNAs that
value would be <10 min at 37°C
(
9,
61). For some genes we
have made an independent determination
of the
t1/2, based on approach-to-equilibrium
labelling; for
RPL3 it is 13 min, and for
RPL30
it is 16.6 min (
23). (Note that
those two genes were known
as Rp1 and Rp73, respectively, at that
time.) This was carried out on
cells growing in a synthetic medium
at 23°C with a doubling time of
132 min, and thus the values are
likely to be an underestimate compared
to those based on cells
growing in YPD at 37°C. Indeed, in our
studies the
t1/2 of the
GAL1-RPL30
mRNA increases from 5 to 11 min as the temperature
is lowered from 37 to 23°C (Table
2).
We suggest, therefore, that the intrinsic
t1/2
of the mRNA encoding L30 is between 5 and 7 min at 37°C. Thus, the
decline
of this mRNA after cells are shifted from 23 to 37°C can be
ascribed
solely to a repression of transcription, without the need to
invoke
an activation of turnover (
15).
The data shown in Fig.
1 to
3 also suggest that the use of the
rpb1-1 mutant may lead to severely misleading estimates of
the
t1/2 of mRNAs. This could be either a
general effect due to
the pleiotropic consequences of halting all Pol
II transcription
or a specific effect on the genes subject to severe
repression.
One might ask why the
t1/2 of RP mRNAs is so
short, since replacing them at frequent intervals seems an unnecessary
use of
resources. Indeed, the
t1/2s of the mRNAs
encoding the abundant
glycolytic enzymes are much longer
(
14). An explanation may
be that the level of production of
RPs must be closely monitored
(
27). Because the RPs
participate in the assembly of a complex
structure and because they are
generally strong RNA-binding proteins,
an excess of an RP may be far
more deleterious to the cell than
an excess of a glycolytic enzyme.
Therefore, it seems likely that
there is selective pressure to maintain
a short
t1/2 for RP mRNAs
in order to more
closely control the relative production of the
many
RPs.
General considerations regarding transcription of RP genes.
Before discussing our data regarding the control of transcription of RP
genes, we argue on two grounds, magnitude and coordination, for the
potential special nature of RP gene transcription and thus for the
likelihood that it has unusual features.
(i) The transcription of ribosomal proteins is a major portion of the
Pol II activity of the cell. As measured by SAGE analysis
(
57), RP genes account for 20 of the 30 most abundant
mRNAs;
each RP gene is represented, on average, by about 30 to 50 mRNAs
per cell (our analysis of data provided by the authors of
reference
57). The 137 RP genes, therefore, would
account for >4,000 of
the mRNAs in the cell. A more direct measurement
has recently
been reported by Holstege et al. (
17). Based on
an estimate
of 15,000 mRNAs per cell, they determined that 132 of the
137
RP genes contributed 4,437 mRNAs, about 30% of the total. This
is
a reasonable number because the ~15,000,000 ribosomal proteins
(~200,000 ribosomes/cell × 78 proteins/ribosome) make up about
15% of the protein mass of the cell, and even more of the protein
number, since they average only ~150 amino acids in length. As
shown
in Table
2, the
t1/2 of an RP mRNA is 5 to 7 min. This
value is consistent with our observations of the effect of
heat
shock on the mRNA levels of many RP genes (
11). It is
also consistent
with the data recently reported by Eisen et al.
(
9), in which
the mRNA level for most RP genes had declined
to less than 20%
of normal by 20 min after a heat shock. Yet, mRNAs
encoding most
other genes have a
t1/2 of >15
min (
17) (based on the use of
the
rpb1-1 allele,
which admittedly may be misleading). Thus,
if RP mRNAs account for 30%
of the total mRNAs yet have a
t1/2 that is
substantially shorter than those of most other mRNAs,
we are led to
conclude that the RP genes account for nearly 50%
of all Pol II
initiation
events.
(ii) As would be expected for genes encoding components of a molecular
machine, the 137 RP genes appear to be regulated in
lockstep (reviewed
in reference
44). This is true of responses
to heat
shock (
11,
24), to a defect in the secretory pathway
(
34 and this paper), to growth conditions such as C
source (
16,
22), to levels of cAMP (
25,
39), and
to the deprivation
of amino acids (
37,
62). During the
growth cycle, RP genes
are repressed as the cells enter late log phase
(
6,
21) and
are induced dramatically within 10 min after
stationary cells
are diluted into a fresh medium (unpublished data). By
using classical
methods no exceptions have been found among the 20 or
so proteins
whose mRNAs have been studied or among the 50 or so
proteins whose
synthesis has been studied in a few situations
(
11). Very recent
data from a genome-wide analysis of a few
conditions, e.g., heat
shock (
9) and diauxie (
6),
suggest that none of the RP genes
escapes from this coordinate
regulation, although a few genes
with apparently intermediate results
will require more direct
analysis.
It is intriguing to consider why
S. cerevisiae has evolved
to utilize transcription as its primary method to regulate the
production of RPs, while both eubacteria (reviewed in reference
64) and vertebrates (reviewed in reference
33) have chosen
to regulate RP synthesis largely at
translation, albeit in very
different ways. Indeed, a recent
transcriptome analysis of mouse
fibroblasts during the transition from
stationary to growth phase
found almost no change in the levels of RP
mRNAs (
19), although
there is a substantial increase in the
rate of RP synthesis (
55).
Role of Rap1p in the repression of RP gene transcription.
Rap1p is the major factor activating the transcription of nearly all of
the RP genes, as well as many other genes with abundant transcripts,
such as those encoding elongation factor 1
(EF1) and the enzymes
of the glycolytic pathway. Rap1p is also the primary element of the
complex that silences both the silent mating type loci and genes
adjacent to telomeres (49). Therefore, Rap1p is a likely
candidate for effecting the silencing of the RP genes in response to
stress. Indeed, we find that just 40 bp containing the two Rap1p
binding sites of the RPL30 gene are sufficient to make the
ACT1 promoter respond like an RP gene to a defect in the
secretory pathway (Fig. 5, construct D). Furthermore, in cells carrying
the rap1-17 allele, which encodes a truncated form of Rap1p
that retains both its DNA binding domains and its activation domain but
not its silencing domain, the RP genes are no longer silenced in
response to a defect in the secretory pathway (35), although
temporary silencing in response to a temperature shift still occurs.
This effect of the rap1-17 allele is also true for genes
that have no Rap1p binding sites, such as RPL3
(35) and construct G shown in Fig. 9A (data not shown). This
observation not only implicates Rap1p in the pathway between the
secretory system and the RP genes but also suggests that a different
pathway is used for the repression of RP gene transcription in response to a temperature shift.
Yet several facts suggest that conventional silencing by Rap1p is not
responsible for the repression of RP genes. Abf1p, rather
than Rap1p,
is the major transcription factor for several RP genes
that are also
repressed in response to a defect in the secretory
pathway, e.g.,
RPL3 (Fig.
1). In addition, Rap1p-mediated silencing
at
telomeres and at silent mating type loci requires Sir3p and
Sir4p
(
31), neither of which is necessary for the silencing
of RP
genes (Fig.
6). Finally, sequences downstream of the Rap1p
binding
sites, adjacent to the promoter of
RPL30, will silence
the
transcription driven by Gal4p, in response to a temperature
shift or to
a defect in the secretory pathway (Fig.
9). These
sequences contain the
putative TATA box and presumably bind TBP
and its associated TAFs, as
well as the sequences adjacent to
the transcription initiation
site.
Thus, our attempts to identify the
cis-acting sequences of
RP genes that mediate the repression of transcription have led
to an
apparent contradiction. Either the Rap1p binding sites or
the
promoter-proximal sequences can play such a role. Yet the
effect of the
rap1-17 allele suggests that Rap1p is necessary
for
silencing in response to a defect in the secretory pathway.
Our
conclusion, then, is that for Rap1p to activate the transcription
of an
RP gene it must bind to upstream sequences, yet for Rap1p
to repress
the transcription of an RP gene it need not bind to
the gene directly.
It remains to be seen how this fascinating
protein can pull off such a
trick.
Whatever the mechanism, the sudden silencing of the RP genes, which
account for 50% of Pol II activity, must have a dramatic
effect on the
overall transcriptional economy of the cell. What
influence does this
sudden release of transcriptional potential
have on the transcription
of other
genes?
| |
ACKNOWLEDGMENTS |
We are grateful to Josep Vilardell for a close reading of the
manuscript, to Ian Willis, Roy Parker, Allan Sachs, Christine Brown,
and Allan Jacobson for useful discussions, to Jung-Hoon Sohn for
communicating unpublished data, to David Shore, Art Lustig, and Myra
Derbyshire for strains and plasmids, and to Mary Studeny and Saqui Huq
for technical assistance.
This research was partially supported by NIH grants GM25532 to J.R.W.
and CA13330 to the Albert Einstein Cancer Center.
| |
FOOTNOTES |
*
Corresponding author. Mailing address: Department of
Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park
Ave., Bronx, NY 10461. Phone: (718) 430-3022. Fax: (718) 430-8574. E-mail: warner{at}aecom.yu.edu.
Present address: Department of Biochemistry and Molecular
Biophysics, Columbia University, College of Physicians and Surgeons, New York, NY 10032.
Present address: Juvenile Diabetes Foundation International, New
York, NY 10005.
| |
REFERENCES |
| 1.
|
Brand, A. H.,
G. Micklem, and K. Nasmyth.
1987.
A yeast silencer contains sequences that can promote autonomous plasmid replication and transcriptional activation.
Cell
51:709-719[Medline].
|
| 2.
|
Caponigro, G., and R. Parker.
1996.
Mechanisms and control of mRNA turnover in Saccharomyces cerevisiae.
Microbiol. Rev.
60:233-249[Free Full Text].
|
| 3.
|
Cavalli, G., and F. Thoma.
1993.
Chromatin transitions during activation and repression of galactose-regulated genes in yeast.
EMBO J.
12:4603-4613[Medline].
|
| 4.
|
Cox, J. S.,
C. E. Shamu, and P. Walter.
1993.
Transcriptional induction of genes encoding endoplasmic reticulum resident proteins requires a transmembrane protein kinase.
Cell
73:1197-1206[Medline].
|
| 5.
|
Derbyshire, M. K.,
K. G. Weinstock, and J. Strathern.
1996.
HST1, a new member of the SIR2 family of genes.
Yeast
12:631-640[Medline].
|
| 6.
|
DeRisi, J. L.,
V. R. Iyer, and P. O. Brown.
1997.
Exploring the metabolic and genetic control of gene expression on a genomic scale.
Science
278:680-686[Abstract/Free Full Text].
|
| 7.
|
Donovan, D. M., and N. J. Pearson.
1986.
Transcriptional regulation of ribosomal proteins during a nutritional upshift in Saccharomyces cerevisiae.
Mol. Cell. Biol.
6:2429-2435[Abstract/Free Full Text].
|
| 8.
|
Dorsman, J. C.,
M. M. Doorenbosch,
C. T. Maurer,
J. H. de Winde,
W. H. Mager,
R. J. Planta, and L. A. Grivell.
1989.
An ARS/silencer binding factor also activates two ribosomal protein genes in yeast.
Nucleic Acids Res.
17:4917-4923[Abstract/Free Full Text].
|
| 9.
|
Eisen, M. B.,
P. T. Spellman,
P. O. Brown, and D. Botstein.
1998.
Cluster analysis and display of genome-wide expression patterns.
Proc. Natl. Acad. Sci. USA
95:14863-14868[Abstract/Free Full Text].
|
| 10.
|
Eng, F. J., and J. R. Warner.
1991.
Structural basis for the regulation of splicing of a yeast messenger RNA.
Cell
65:797-804[Medline].
|
| 11.
|
Gorenstein, C., and J. R. Warner.
1976.
Coordinate regulation of the synthesis of eukaryotic ribosomal proteins.
Proc. Natl. Acad. Sci. USA
73:1547-1551[Abstract/Free Full Text].
|
| 12.
|
Greenberg, J. R.
1972.
High stability of messenger RNA in growing cultured cells.
Nature
240:102-104[Medline].
|
| 13.
|
Hamil, K. G.,
H. G. Nam, and H. M. Fried.
1988.
Constitutive transcription of yeast ribosomal protein gene TCM1 is promoted by uncommon cis- and trans-acting elements.
Mol. Cell. Biol.
8:4328-4341[Abstract/Free Full Text].
|
| 14.
|
Herrick, D.,
R. Parker, and A. Jacobson.
1990.
Identification and comparison of stable and unstable mRNAs in Saccharomyces cerevisiae.
Mol. Cell. Biol.
10:2269-2284[Abstract/Free Full Text].
|
| 15.
|
Herruer, M. H.,
W. H. Mager,
H. A. Raue,
P. Vreken,
E. Wilms, and R. J. Planta.
1988.
Mild temperature shock affects transcription of yeast ribosomal protein genes as well as the stability of their mRNAs.
Nucleic Acids Res.
16:7917-7929[Abstract/Free Full Text].
|
| 16.
|
Herruer, M. H.,
W. H. Mager,
L. P. Woudt,
R. T. Nieuwint,
G. M. Wassenaar,
P. Groeneveld, and R. J. Planta.
1987.
Transcriptional control of yeast ribosomal protein synthesis during carbon-source upshift.
Nucleic Acids Res.
15:10133-10144[Abstract/Free Full Text].
|
| 17.
|
Holstege, F. C. P.,
E. G. Jennings,
J. J. Wyrick,
T. I. Lee,
C. J. Hengartner,
M. R. Green,
T. R. Golub,
E. S. Lander, and R. A. Young.
1998.
Dissecting the regulatory circuitry of a eukaryotic genome.
Cell
95:717-728[Medline].
|
| 18.
|
Imai, Y.,
Y. Matsushima,
T. Sugimura, and M. Terada.
1991.
A simple and rapid method for generating a deletion by PCR.
Nucleic Acids Res.
19:2785[Free Full Text].
|
| 19.
|
Iyer, V. R.,
M. B. Eisen,
D. T. Ross,
G. Schuler,
T. Moore,
J. C. F. Lee,
J. M. Trent,
L. M. Staudt,
J. Hudson,
M. S. Boguski,
D. A. Lashkari,
D. Shalon,
D. Botstein, and P. O. Brown.
1999.
The transcriptional program in response of human fibroblasts to serum.
Science
283:83-87[Abstract/Free Full Text].
|
| 20.
|
Johnston, M., and M. Carlson.
1992.
Regulation of carbon and phosphate utilization, p. 193-281.
In
E. W. Jones, J. R. Pringle, and J. R. Broach (ed.), The molecular and cellular biology of the yeast Saccharomyces: gene expression. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
|
| 21.
|
Ju, Q., and J. R. Warner.
1994.
Ribosome synthesis during the growth cycle of Saccharomyces cerevisiae.
Yeast
10:151-157[Medline].
|
| 22.
|
Kief, D. R., and J. R. Warner.
1981.
Coordinate control of syntheses of ribosomal ribonucleic acid and ribosomal proteins during nutritional shift-up in Saccharomyces cerevisiae.
Mol. Cell. Biol.
1:1007-1015[Abstract/Free Full Text].
|
| 23.
|
Kim, C. H., and J. R. Warner.
1983.
Messenger RNA for ribosomal proteins in yeast.
J. Mol. Biol.
165:79-89[Medline].
|
| 24.
|
Kim, C. H., and J. R. Warner.
1983.
Mild temperature shock alters the transcription of a discrete class of Saccharomyces cerevisiae genes.
Mol. Cell. Biol.
3:457-465[Abstract/Free Full Text].
|
| 25.
|
Klein, C., and K. Struhl.
1994.
Protein kinase A mediates growth-regulated expression of yeast ribosomal protein genes by modulating RAP1 transcriptional activity.
Mol. Cell. Biol.
14:1920-1928[Abstract/Free Full Text].
|
| 26.
|
Lascaris, R. F.,
W. H. Mager, and R. J. Planta.
1999.
DNA-binding requirements of the yeast protein Rap1p as selected in silico from ribosomal gene promoter sequences.
Bioinformatics
15:267-277[Abstract/Free Full Text].
|
| 27.
|
Li, B.,
J. Vilardell, and J. R. Warner.
1996.
An RNA structure involved in feedback regulation of splicing and of translation is critical for biological fitness.
Proc. Natl. Acad. Sci. USA
93:1596-1600[Abstract/Free Full Text].
|
| 28.
|
Li, B., and J. R. Warner.
1996.
Mutation of the Rab6 homologue of Saccharomyces cerevisiae, YPT6, inhibits both early Golgi function and ribosome biosynthesis.
J. Biol. Chem.
271:16813-16819[Abstract/Free Full Text].
|
| 29.
|
Liang, S.,
F. Lacroute, and F. Kepes.
1993.
Multicopy STS1 restores both protein transport and ribosomal RNA stability in a new yeast sec23 mutant allele.
Eur. J. Cell Biol.
62:270-281[Medline].
|
| 30.
|
Lohr, D.,
P. Venkov, and J. Zlatanova.
1995.
Transcriptional regulation in the yeast GAL gene family: a complex genetic network.
FASEB J.
9:777-787[Abstract].
|
| 31.
|
Lustig, A. J.
1998.
Mechanisms of silencing in Saccharomyces cerevisiae.
Curr. Opin. Genet. Dev.
8:233-239[Medline].
|
| 32.
|
Mager, W. H.,
R. J. Planta,
J. P. Ballesta,
J. C. Lee,
K. Mizuta,
K. Suzuki,
J. R. Warner, and J. L. Woolford, Jr.
1997.
A new nomenclature for the cytoplasmic ribosomal proteins of Saccharomyces cerevisiae.
Nucleic Acids Res.
25:4872-4875[Abstract/Free Full Text].
|
| 33.
|
Meyuhas, O.,
D. Avni, and S. Shama.
1996.
Translational control of ribosomal protein mRNAs in eukaryotes, p. 363-388.
In
J. W. B. Hershey, M. B. Mathews, and N. Sonenberg (ed.), Translational control. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
|
| 33a.
| MIPS. 26 January 1998, posting date. Yeast a new
nomenclature for the cytoplasmic ribosomal proteins of
Saccharomyces cerevisiae. [Online.]
http://www.mips.biochem.mpg.de/proj/yeast/reviews/rib_nomencl.html. [8
June 1999, last date accessed.]
|
| 34.
|
Mizuta, K.,
T. Hashimoto,
K. Suzuki, and E. Otaka.
1991.
Yeast ribosomal proteins. XII. YS11 of Saccharomyces cerevisiae is a homologue to E. coli S4 according to the gene analysis.
Nucleic Acids Res.
19:2603-2608.
|
| 35.
|
Mizuta, K.,
R. Tsujii,
J. R. Warner, and M. Nishiyama.
1998.
The C-terminal silencing domain of Rap1p is essential for the repression of ribosomal protein genes in response to a defect in the secretory pathway.
Nucleic Acids Res.
26:1063-1069[Abstract/Free Full Text].
|
| 36.
|
Mizuta, K., and J. R. Warner.
1994.
Continued functioning of the secretory pathway is essential for ribosome synthesis.
Mol. Cell. Biol.
14:2493-2502[Abstract/Free Full Text].
|
| 37.
|
Moehle, C. M., and A. G. Hinnebusch.
1991.
Association of RAP1 binding sites with stringent control of ribosomal protein gene transcription in Saccharomyces cerevisiae.
Mol. Cell. Biol.
11:2723-2735[Abstract/Free Full Text].
|
| 38.
|
Moretti, P.,
K. Freeman,
L. Coodly, and D. Shore.
1994.
Evidence that a complex of SIR proteins interacts with the silencer and telomere-binding protein RAP1.
Genes Dev.
8:2257-2269[Abstract/Free Full Text].
|
| 39.
|
Neuman-Silberberg, F. S.,
S. Bhattacharya, and J. R. Broach.
1995.
Nutrient availability and the RAS/cyclic AMP pathway both induce expression of ribosomal protein genes in Saccharomyces cerevisiae but by different mechanisms.
Mol. Cell. Biol.
15:3187-3196[Abstract].
|
| 40.
|
Nierras, C. R., and J. R. Warner.
1999.
Protein kinase C enables the regulatory circuit that connects membrane synthesis to ribosome synthesis in S. cerevisiae.
J. Biol. Chem.
274:13235-13241[Abstract/Free Full Text].
|
| 41.
|
Nieuwint, R. T.,
W. H. Mager,
K. C. Maurer, and R. J. Planta.
1989.
Mutational analysis of the upstream activation site of yeast ribosomal protein genes.
Curr. Genet.
15:247-251[Medline].
|
| 42.
|
Nonet, M.,
C. Scafe,
J. Sexton, and R. Young.
1987.
Eukaryotic RNA polymerase conditional mutant that rapidly ceases mRNA synthesis.
Mol. Cell. Biol.
7:1602-1611[Abstract/Free Full Text].
|
| 43.
|
Parker, R.,
D. Herrick,
S. W. Peltz, and A. Jacobson.
1991.
Measurement of mRNA decay rates in Saccharomyces cerevisiae.
Methods Enzymol.
194:415-423[Medline].
|
| 44.
|
Planta, R. J.
1997.
Regulation of ribosome synthesis in yeast.
Yeast
13:1505-1518[Medline].
|
| 45.
|
Rotenberg, M. O., and J. L. Woolford, Jr.
1986.
Tripartite upstream promoter element essential for expression of Saccharomyces cerevisiae ribosomal protein genes.
Mol. Cell. Biol.
6:674-687[Abstract/Free Full Text].
|
| 46.
|
Schmitt, M. E.,
T. A. Brown, and B. L. Trumpower.
1990.
A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae.
Nucleic Acids Res.
18:3091-3092[Free Full Text].
|
| 47.
|
Schwindinger, W. F., and J. R. Warner.
1987.
Transcriptional elements of the yeast ribosomal protein gene CYH2.
J. Biol. Chem.
262:5690-5695[Abstract/Free Full Text].
|
| 48.
|
Shen, W.-C., and M. R. Green.
1997.
Yeast TAFII145 functions as a core promoter selectivity factor, not a general coactivator.
Cell
90:615-624[Medline].
|
| 49.
|
Shore, D.
1994.
RAP1: a protean regulator in yeast.
Trends Genet.
10:408-412[Medline].
|
| 50.
|
Shore, D., and K. A. Nasmyth.
1987.
Purification and cloning of a DNA binding protein from yeast that binds to both silencer and activator elements.
Cell
51:721-732[Medline].
|
| 51.
|
Sikorski, R. S., and P. Hieter.
1989.
A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae.
Genetics
122:19-27[Abstract/Free Full Text].
|
| 52.
|
Smith, J. S., and J. D. Boeke.
1997.
An unusual form of transcriptional silencing in yeast ribosomal DNA.
Genes Dev.
11:241-254[Abstract/Free Full Text].
|
| 53.
|
Sussel, L., and D. Shore.
1991.
Separation of transcriptional activation and silencing functions of the RAP1-encoded repressor/activator protein 1: isolation of viable mutants affecting both silencing and telomere length.
Proc. Natl. Acad. Sci. USA
88:7749-7753[Abstract/Free Full Text].
|
| 54.
|
Thomas, B. J., and R. Rothstein.
1989.
Elevated recombination rates in transcriptionally active DNA.
Cell
56:619-630[Medline].
|
| 55.
|
Tushinski, R. J., and J. R. Warner.
1982.
Ribosomal proteins are synthesized preferentially in cells commencing growth.
J. Cell. Physiol.
112:128-135[Medline].
|
| 56.
|
Udem, S. A., and J. R. Warner.
1972.
Ribosomal RNA synthesis in Saccharomyces cerevisiae.
J. Mol. Biol.
65:227-242[Medline].
|
| 57.
|
Velculescu, V. E.,
L. Zhang,
W. Zhou,
J. Vogelstein,
M. A. Basrai,
D. E. Bassett, Jr.,
P. Hieter,
B. Vogelstein, and K. W. Kinzler.
1997.
Characterization of the yeast transcriptome.
Cell
88:243-251[Medline].
|
| 58.
|
Vilardell, J., and J. R. Warner.
1994.
Regulation of splicing at an intermediate step in the formation of the spliceosome.
Genes Dev.
8:211-220[Abstract/Free Full Text].
|
| 59.
|
Warner, J. R.
1989.
Synthesis of ribosomes in Saccharomyces cerevisiae.
Microbiol. Rev.
53:256-271[Abstract/Free Full Text].
|
| 60.
|
Warner, J. R.
1991.
Labeling of RNA and phosphoproteins in Saccharomyces cerevisiae.
Methods Enzymol.
194:423-428[Medline].
|
| 61.
|
Warner, J. R., and C. Gorenstein.
1977.
The synthesis of eucaryotic ribosomal proteins in vitro.
Cell
11:201-212[Medline].
|
| 62.
|
Warner, J. R., and C. Gorenstein.
1978.
Yeast has a true stringent response.
Nature
275:338-339[Medline].
|
| 63.
|
Wright, J. H.,
D. E. Gottschling, and V. A. Zakian.
1992.
Saccharomyces telomeres assume a non-nucleosomal chromatin structure.
Genes Dev.
6:197-210[Abstract/Free Full Text].
|
| 64.
|
Zengel, J. M., and L. Lindahl.
1994.
Diverse mechanisms for regulating ribosomal protein synthesis in Escherichia coli.
Prog. Nucleic Acid Res. Mol. Biol.
47:331-370[Medline].
|
Molecular and Cellular Biology, August 1999, p. 5393-5404, Vol. 19, No. 8
0270-7306/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.
This article has been cited by other articles:
-
Cohen, T. J., Mallory, M. J., Strich, R., Yao, T.-P.
(2008). Hos2p/Set3p Deacetylase Complex Signals Secretory Stress through the Mpk1p Cell Integrity Pathway. Eukaryot Cell
7: 1191-1199
[Abstract]
[Full Text]
-
Mavrich, T. N., Ioshikhes, I. P., Venters, B. J., Jiang, C., Tomsho, L. P., Qi, J., Schuster, S. C., Albert, I., Pugh, B. F.
(2008). A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res
18: 1073-1083
[Abstract]
[Full Text]
-
Li, S., Ding, B., Chen, R., Ruggiero, C., Chen, X.
(2006). Evidence that the Transcription Elongation Function of Rpb9 Is Involved in Transcription-Coupled DNA Repair in Saccharomyces cerevisiae. Mol. Cell. Biol.
26: 9430-9441
[Abstract]
[Full Text]
-
Zanton, S. J., Pugh, B. F.
(2006). Full and partial genome-wide assembly and disassembly of the yeast transcription machinery in response to heat shock.. Genes Dev.
20: 2250-2265
[Abstract]
[Full Text]
-
Zhao, Y., McIntosh, K. B., Rudra, D., Schawalder, S., Shore, D., Warner, J. R.
(2006). Fine-structure analysis of ribosomal protein gene transcription.. Mol. Cell. Biol.
26: 4853-4862
[Abstract]
[Full Text]
-
Hall, D. B., Wade, J. T., Struhl, K.
(2006). An HMG Protein, Hmo1, Associates with Promoters of Many Ribosomal Protein Genes and throughout the rRNA Gene Locus in Saccharomyces cerevisiae.. Mol. Cell. Biol.
26: 3672-3679
[Abstract]
[Full Text]
-
Samanta, M. P., Tongprasit, W., Sethi, H., Chin, C.-S., Stolc, V.
(2006). Global identification of noncoding RNAs in Saccharomyces cerevisiae by modulating an essential RNA processing pathway.. Proc. Natl. Acad. Sci. USA
103: 4192-4197
[Abstract]
[Full Text]
-
Santangelo, G. M.
(2006). Glucose Signaling in Saccharomyces cerevisiae. Microbiol. Mol. Biol. Rev.
70: 253-282
[Abstract]
[Full Text]
-
Lotan, R., Bar-On, V. G., Harel-Sharvit, L., Duek, L., Melamed, D., Choder, M.
(2005). The RNA polymerase II subunit Rpb4p mediates decay of a specific class of mRNAs. Genes Dev.
19: 3004-3016
[Abstract]
[Full Text]
-
Smirnova, J. B., Selley, J. N., Sanchez-Cabo, F., Carroll, K., Eddy, A. A., McCarthy, J. E. G., Hubbard, S. J., Pavitt, G. D., Grant, C. M., Ashe, M. P.
(2005). Global Gene Expression Profiling Reveals Widespread yet Distinctive Translational Responses to Different Eukaryotic Translation Initiation Factor 2B-Targeting Stress Pathways. Mol. Cell. Biol.
25: 9340-9349
[Abstract]
[Full Text]
-
Yu, T., Li, K.-C.
(2005). Inference of transcriptional regulatory network by two-stage constrained space factor analysis. Bioinformatics
21: 4033-4038
[Abstract]
[Full Text]
-
CULBERTSON, M. R., NEENO-ECKWALL, E.
(2005). Transcript selection and the recruitment of mRNA decay factors for NMD in Saccharomyces cerevisiae. RNA
11: 1333-1339
[Abstract]
[Full Text]
-
Grigull, J., Mnaimneh, S., Pootoolal, J., Robinson, M. D., Hughes, T. R.
(2004). Genome-Wide Analysis of mRNA Stability Using Transcription Inhibitors and Microarrays Reveals Posttranscriptional Control of Ribosome Biogenesis Factors. Mol. Cell. Biol.
24: 5534-5547
[Abstract]
[Full Text]
-
Sakaki, K., Tashiro, K., Kuhara, S., Mihara, K.
(2003). Response of Genes Associated with Mitochondrial Function to Mild Heat Stress in Yeast Saccharomyces cerevisiae. J Biochem
134: 373-384
[Abstract]
[Full Text]
-
Zhao, Y., Sohn, J.-H., Warner, J. R.
(2003). Autoregulation in the Biosynthesis of Ribosomes. Mol. Cell. Biol.
23: 699-707
[Abstract]
[Full Text]
-
Mariadason, J. M., Arango, D., Corner, G. A., Aranes, M. J., Hotchkiss, K. A., Yang, W., Augenlicht, L. H.
(2002). A Gene Expression Profile That Defines Colon Cell Maturation in Vitro. Cancer Res.
62: 4791-4804
[Abstract]
[Full Text]
-
Lee, S.-W., Berger, S. J., Martinovic', S., Pasa-Tolic', L., Anderson, G. A., Shen, Y., Zhao, R., Smith, R. D.
(2002). Direct mass spectrometric analysis of intact proteins of the yeast large ribosomal subunit using capillary LC/FTICR. Proc. Natl. Acad. Sci. USA
99: 5942-5947
[Abstract]
[Full Text]
-
Kim, M. J., Kim, J. B., Kim, D. S., Park, S. D.
(2002). Glucose-inducible expression of rrg1+ in Schizosaccharomyces pombe: post-transcriptional regulation of mRNA stability mediated by the downstream region of the poly(A) site. Nucleic Acids Res
30: 1145-1153
[Abstract]
[Full Text]
-
Fleming, J. A., Lightcap, E. S., Sadis, S., Thoroddsen, V., Bulawa, C. E., Blackman, R. K.
(2002). Complementary whole-genome technologies reveal the cellular response to proteasome inhibition by PS-341. Proc. Natl. Acad. Sci. USA
99: 1461-1466
[Abstract]
[Full Text]
-
Jansen, R., Greenbaum, D., Gerstein, M.
(2002). Relating Whole-Genome Expression Data with Protein-Protein Interactions. Genome Res
12: 37-46
[Abstract]
[Full Text]
-
Wade, C., Shea, K. A., Jensen, R. V., McAlear, M. A.
(2001). EBP2 Is a Member of the Yeast RRB Regulon, a Transcriptionally Coregulated Set of Genes That Are Required for Ribosome and rRNA Biosynthesis. Mol. Cell. Biol.
21: 8638-8650
[Abstract]
[Full Text]
-
Miyao, T., Barnett, J. D., Woychik, N. A.
(2001). Deletion of the RNA Polymerase Subunit RPB4 Acts as a Global, Not Stress-specific, Shut-off Switch for RNA Polymerase II Transcription at High Temperatures. J. Biol. Chem.
276: 46408-46413
[Abstract]
[Full Text]
-
Miyoshi, K., Miyakawa, T., Mizuta, K.
(2001). Repression of rRNA synthesis due to a secretory defect requires the C-terminal silencing domain of Rap1p in Saccharomyces cerevisiae. Nucleic Acids Res
29: 3297-3303
[Abstract]
[Full Text]
-
Hendrick, J. L., Wilson, P. G., Edelman, I. I., Sandbaken, M. G., Ursic, D., Culbertson, M. R.
(2001). Yeast Frameshift Suppressor Mutations in the Genes Coding for Transcription Factor Mbf1p and Ribosomal Protein S3: Evidence for Autoregulation of S3 Synthesis. Genetics
157: 1141-1158
[Abstract]
[Full Text]
-
Iouk, T. L., Aitchison, J. D., Maguire, S., Wozniak, R. W.
(2001). Rrb1p, a Yeast Nuclear WD-Repeat Protein Involved in the Regulation of Ribosome Biosynthesis. Mol. Cell. Biol.
21: 1260-1271
[Abstract]
[Full Text]
-
Kuhn, K. M., DeRisi, J. L., Brown, P. O., Sarnow, P.
(2001). Global and Specific Translational Regulation in the Genomic Response of Saccharomyces cerevisiae to a Rapid Transfer from a Fermentable to a Nonfermentable Carbon Source. Mol. Cell. Biol.
21: 916-927
[Abstract]
[Full Text]
-
Causton, H. C., Ren, B., Koh, S. S., Harbison, C. T., Kanin, E., Jennings, E. G., Lee, T. I., True, H. L., Lander, E. S., Young, R. A.
(2001). Remodeling of Yeast Genome Expression in Response to Environmental Changes. Mol. Biol. Cell
12: 323-337
[Abstract]
[Full Text]
-
WARNER, J.R., VILARDELL, J., SOHN, J.H.
(2001). Economics of Ribosome Biosynthesis. Cold Spring Harb Symp Quant Biol
66: 567-574
[Abstract]
-
Gasch, A. P., Spellman, P. T., Kao, C. M., Carmel-Harel, O., Eisen, M. B., Storz, G., Botstein, D., Brown, P. O.
(2000). Genomic Expression Programs in the Response of Yeast Cells to Environmental Changes. Mol. Biol. Cell
11: 4241-4257
[Abstract]
[Full Text]
-
Jelinsky, S. A., Estep, P., Church, G. M., Samson, L. D.
(2000). Regulatory Networks Revealed by Transcriptional Profiling of Damaged Saccharomyces cerevisiae Cells: Rpn4 Links Base Excision Repair with Proteasomes. Mol. Cell. Biol.
20: 8157-8167
[Abstract]
[Full Text]
-
ALLAN, M. F., NIELSEN, M. K., POMP, D.
(2000). Gene expression in hypothalamus and brown adipose tissue of mice divergently selected for heat loss. Physiol. Genomics
3: 149-156
[Abstract]
[Full Text]
-
Burger, F., Daugeron, M.-C., Linder, P.
(2000). Dbp10p, a putative RNA helicase from Saccharomyces cerevisiae, is required for ribosome biogenesis. Nucleic Acids Res
28: 2315-2323
[Abstract]
[Full Text]
-
Li, Y., Moir, R. D., Sethy-Coraci, I. K., Warner, J. R., Willis, I. M.
(2000). Repression of Ribosome and tRNA Synthesis in Secretion-Defective Cells Is Signaled by a Novel Branch of the Cell Integrity Pathway. Mol. Cell. Biol.
20: 3843-3851
[Abstract]
[Full Text]
-
Kuras, L., Kosa, P., Mencia, M., Struhl, K.
(2000). TAF-Containing and TAF-Independent Forms of Transcriptionally Active TBP in Vivo. Science
288: 1244-1248
[Abstract]
[Full Text]
-
Rep, M., Krantz, M., Thevelein, J. M., Hohmann, S.
(2000). The Transcriptional Response of Saccharomyces cerevisiae to Osmotic Shock. Hot1p AND Msn2p/Msn4p ARE REQUIRED FOR THE INDUCTION OF SUBSETS OF HIGH OSMOLARITY GLYCEROL PATHWAY-DEPENDENT GENES. J. Biol. Chem.
275: 8290-8300
[Abstract]
[Full Text]
-
Nanduri, J., Mitra, S., Andrei, C., Liu, Y., Yu, Y., Hitomi, M., Tartakoff, A. M.
(1999). An Unexpected Link between the Secretory Path and the Organization of the Nucleus. J. Biol. Chem.
274: 33785-33789
[Abstract]
[Full Text]
-
Yu, X., Warner, J. R.
(2001). Expression of a Micro-protein. J. Biol. Chem.
276: 33821-33825
[Abstract]
[Full Text]
Top
Abstract
Introduction
