Recently, we identified War1p as the dedicated transcriptional regulator required for PDR12 stress induction.. Importantly, in contrast with wild-type War1p, War1-42p is also no longer ph
Trang 1gene, linking transcription factor phosphorylation
to weak-acid stress adaptation
Christa Gregori*, Bettina Bauer*, Chantal Schwartz, Angelika Kren, Christoph Schu¨ller§
and Karl Kuchler
Medical University Vienna, Max F Perutz Laboratories, Department of Medical Biochemistry, Campus Vienna Biocenter, Austria
Weak acids have a long history as additives in food
preservation In addition to sulfites used in wine
mak-ing, acetic, sorbic, benzoic and propionic acids are
commonly used in the food and beverage industry
to prevent spoilage [1,2] In solution, weak acids exist
in a dynamic equilibrium between undissociated, uncharged molecules and their anionic form These acids display increased antimicrobial action at low pH, which favors the undissociated state The uncharged molecules can readily diffuse through the plasma
Keywords
ABC transporter; stress response; weak
organic acids; yeast; zinc finger
Correspondence
K Kuchler, Medical University Vienna, Max
F Perutz Laboratories, Department of
Medical Biochemistry, Campus Vienna
Biocenter, Dr Bohr-Gasse 9 ⁄ 2, A-1030,
Vienna, Austria
Fax: +43 1 4277 9618
Tel: +43 1 4277 61807
E-mail: karl.kuchler@meduniwien.ac.at
Present address
Universite´ de Nice-Sophia Antipolis,
Inserm, U636, Centre de Biochimie, UFR
Sciences, Parc Valrose, Nice, France
Institute of Biochemistry and Genetics,
Department of Clinical and Biological
Research (DKBW), Basel, Switzerland
§University of Vienna, Max F Perutz
Laboratories, Department of Biochemistry &
Molecular and Cellular Biology, Campus
Vienna Biocenter, Austria
* These authors contributed equally to this
work
(Received 11 January 2007, revised 4 April
2007, accepted 19 April 2007)
doi:10.1111/j.1742-4658.2007.05837.x
Exposure of the yeast Saccharomyces cerevisiae to weak organic acids such
as the food preservatives sorbate, benzoate and propionate leads to the pronounced induction of the plasma membrane ATP-binding cassette (ABC) transporter, Pdr12p This protein mediates efflux of weak acid ani-ons, which is essential for stress adaptation Recently, we identified War1p
as the dedicated transcriptional regulator required for PDR12 stress induction Here, we report the results from a genetic screen that led to the isolation of two war1 alleles encoding mutant variants, War1-28p and War1-42p, which are unable to support cell growth in the presence of sorb-ate DNA sequencing revealed that War1-28 encodes a truncated form of the transcriptional regulator, and War1-42 carries three clustered mutations near the C-terminal activation domain Although War1-42 is expressed and properly localized in the nucleus, the War1-42p variant fails to bind the weak-acid-response elements in the PDR12 promoter, as shown by in vivo footprinting Importantly, in contrast with wild-type War1p, War1-42p is also no longer phosphorylated upon weak-acid challenge, demonstrating that phosphorylation of War1p, its activation and DNA binding are tightly linked processes that are essential for adaptation to weak-acid stress
Abbreviations
GST, glutathione S-transferase; MHR, middle homology region; NLS, nuclear localization signal; PDR, pleiotropic drug resistance; WARE, weak-acid-response element; YPD, yeast peptone ⁄ dextrose.
Trang 2membrane In the cytoplasm, weak acids encounter a
more neutral pH, causing their dissociation into acid
anions and protons The protons lead to cytoplasmic
acidification, thereby inhibiting important metabolic
processes such as glycolysis [3], possibly interfering
with active transport and signal transduction [1]
Fur-thermore, sorbate and benzoate may also act as
membrane-damaging substances [4] and, at least under
aerobic conditions, cause severe oxidative stress [5,6]
The antimicrobial action of weak-acid preservatives
is usually characterized by extended lag phases and cell
stasis, although microbial killing does not occur
How-ever, cells can adapt to the presence of weak acid and
resume growth In Saccharomyces cerevisiae, this
adap-tation requires induction of the Pdr12p plasma
mem-brane ATP-binding cassette (ABC) transporter [7]
Together with the plasma membrane H+-ATPase,
Pma1p, the activity of which is also regulated by weak
acid stress [8,9], Pdr12p becomes one of the most
abun-dant surface proteins in stressed cells [7] Whereas
Pma1p effluxes protons, Pdr12p mediates cellular
extrusion of weak acid anions [7] Notably, other
mem-bers of the fungal ABC transporter family transport a
wide variety of different xenobiotics across the plasma
membrane or membranes of subcellular compartments
[10,11] Pdr12p is the essential component of this stress
response pathway, as cells are hypersensitive to sorbic,
benzoic and propionic acid [7] and fail to adapt to such
stress conditions in the absence of Pdr12p Moreover,
recent data indicate the involvement of Pdr12p in the
export of by-products of amino-acid catabolism, as a
pdr12D strain displays hypersensitivity to fusel acids
derived from leucine, isoleucine, valine, phenylalanine
and tryptophan [12] Therefore, Pdr12p is not only
required for adaptation to weak-acid stress, but might
also efflux weak-acid metabolites Notably, PDR12 is
rapidly induced by weak-acid challenge [7], but also in
cultures grown with leucine, methionine or
phenylalan-ine as sole nitrogen source [12] A recent study [13]
attempted to identify Pdr12p-like proteins in other food
spoilage yeasts A sorbic-inducible protein
cross-react-ing with S cerevisiae Pdr12p antibodies in
Saccharomy-ces bayanuswas found In contrast, proteins detectable
with the same antibodies in Zygosaccharomyces bailii
and Zygosaccharomyces lentus were not up-regulated
upon sorbate challenge
We are interested in identifying components of the
signaling pathway required for this efficient response in
S cerevisiae Hence, we pursued two different strategies
First, we used a functional genomics approach and
screened all putative nonessential transcription factor
deletions of the EUROSCARF collection [14] (http://
www.uni-frankfurt.de/fb15/mikro/eroscarf/) for sorbate
hypersensitivity This approach identified the regulator War1p (weak acid resistance) as the main inducer of PDR12 [15] War1p is a nuclear transcription factor, which decorates at least one weak-acid-response element (WARE) in the PDR12 promoter War1p is rapidly phosphorylated upon stress challenge, and phosphory-lation is somehow coupled to War1p activation [15] Interestingly, War1p is required for PDR12 up-regu-lation in response to exogenous weak-acid stress, but it appears also to be involved in the metabolism-derived endogenous fusel acid stress response [12]
The War1p protein belongs to the fungal-specific Zn(II)2Cys6zinc finger family of transcriptional regula-tors with some 54 other putative members in S cere-visiae [16] These are implicated in various important cellular processes, including amino-acid [17] and galac-tose [18] metabolism, nitrogen source utilization [16], peroxisomal proliferation [19,20], respiration [21,22] and even pleiotropic drug resistance (PDR) [11] For example, Pdr1p and Pdr3p are key players in yeast PDR development, because they control ABC drug efflux pumps such as Pdr5p [23,24], Snq2p [25,26] and Yor1p [27], all of which are involved in PDR [10,11] Most regulators harbor a binuclear DNA-binding zinc cluster at the N-terminus, whereas the acidic activation domain is usually present at the C-terminus The mid-dle homology region (MHR) bridging the DNA-bind-ing and the activation domain may control the activity
or specificity of the transcription factor, as deletions or mutations in this region often result in constitutive activity [22,28–30] Notably, a WAR1 orthologue has been identified in the human fungal pathogen Candida albicans [31] Consistent with its role in S cerevisiae, this WAR1 is also required for sorbate tolerance Moreover, our group recently identified the Candida glabrata homologue of War1p (C Gregori and
K Kuchler, unpublished work) Preliminary experi-ments show that it is also required for a response to weak organic acids in the human fungal pathogen
C glabrata, demonstrating the evolutionary conserva-tion of this weak-acid stress in the fungal kingdom (C Gregori and K Kuchler, unpublished work) Secondly, we applied a classical genetic screen using
a PDR12prom-lacZ reporter gene to identify compo-nents of the weak-acid response pathway Here, we report the results of the genetic approach, which leads
to the isolation of two war1 mutant alleles that are unable to drive Pdr12p induction Remarkably, the genetic screen identified mutations in the WAR1 gene only, indicating that weak-acid stress response requires two major components, a dedicated stress regulator and the Pdr12p efflux pump The defective War1-42p mutant is no longer phosphorylated upon stress and
Trang 3unable to bind to cis-acting WARE motifs, suggesting
that activation of War1p or its binding to WARE is
tightly linked to its post-translational modification
Results
Isolation of sorbate-sensitive mutant strains
To identify components of the stress response pathway
that mediates induction of the Pdr12p efflux pump, we
set up a classical mutagenesis screen For the isolation
of mutant cells that fail to induce PDR12 upon weak
acid challenge, we constructed a reporter strain carrying
the lacZ gene driven by the PDR12 promoter integrated
into the ura3 loci of two different genetic backgrounds,
creating the strains YCS12ZI and YAK3 These strains
were grown to the exponential growth phase, plated
and irradiated with UV light to randomly introduce
mutations After a 2-day incubation, colonies were
replica-plated on plates containing 5 mm sorbate and
the dye X-Gal to induce the PDR12 promoter and to
visualize LacZ expression In a first round of screening,
we obtained 111 white colonies (62 for YAK3 and 49
for YCS12Z-I) To determine if the white color resulted
from a lack of PDR12 promoter induction, and thus no
expression of lacZ, these colonies were re-screened for
their Pdr12p protein concentrations by
immuno-blotting Although several mutants showed reduced
Pdr12p concentrations under stress conditions (data not
shown), only two mutant strains, 42 and 28, lacked
detectable Pdr12p induction upon sorbate stress
(Fig 1A) Both mutants were back-crossed with the
wild-type several times to clean up the genetic
back-ground and determine whether the phenotype was
caused by mutations in a single gene As tetrad analysis
revealed a 2 : 2 cosegregation of sorbate sensitivity with
the inability of lacZ induction, both mutations must
reside in a single gene (data not shown)
Growth-inhibi-tion assays (Fig 1B) showed that mutants 28 and 42
grew at a sorbate concentration of up to 0.25 mm The
pdr12D control strain was viable, but exhibited reduced
growth on 0.5 mm sorbate plates, and failed to grow on
1 mm sorbate, whereas the wild-type control even grew
at concentrations above 1 mm Therefore, we isolated
two yeast mutants with defects in a single gene
repre-senting at least one component of the weak-acid
response machinery that acts through Pdr12p induction
to trigger adaptation
Identification of mutated genes
In addition to the classical genetic approach, we
recently pursued a functional genomics approach to
identify regulators of weak organic acid resistance Making use of the EUROSCARF haploid deletion strain collection of S cerevisiae [14] (EUROSCARF, Germany; http//http://www.uni-frankfurt.de/fb15/ mikro/euroscarf/), we tested all viable transcription factor deletion strains for their ability to grow in the presence of sorbic acid This approach identified the transcription factor essential for Pdr12p induction and hence weak-acid resistance, War1p [15] To determine
if the mutants isolated in the classical genetic screen are allelic to WAR1, appropriate selection markers were integrated and the strains subjected to com-plementation analysis Figure 2 shows the growth phenotypes of the resulting diploid strains on yeast pep-tone⁄ dextrose (YPD), pH 4.5, with different sorbate
A
B
WT war1-28 war1-42 pdr12Δ
WT
war1-28 war1-42 pdr12Δ
YPD pH 4.5 control
+ Sorbate
Pdr12p control
sorbate
Fig 1 war1 mutants are sorbate-sensitive and fail to induce Pdr12p upon sorbate stress (A) The strains W303-1A (WT), YAK4 (War1-28), YCS42-D4 (War1-42) and control strain YBB14 (pdr12D) were grown in YPD to an A 600 of 1 The cultures were split and one half was stressed with 8 m M sorbate for 1 h Cell extracts equivalent to 0.5 A600were separated by SDS ⁄ PAGE (7% gel), and the immunoblots were decorated with polyclonal anti-Pdr12p serum A cross-reaction to the antibodies served as loading control (B) The strains W303-1A (WT), YAK4 28), YCS42-D4 (War1-42) and YBB14 (pdr12D) were grown in YPD to an A600 of 1 Then the A 600 was adjusted to 0.2, and the cells were spotted along with three 1 : 10 serial dilutions on YPD, pH 4.5, containing the indicated sorbate concentrations Growth was monitored after
a 48-h incubation at 30 C.
Trang 4concentrations Mutants 28 and 42, as well as the
war1D deletion, when in combination with a wild-type
gene, displayed similar growth to the diploid wild-type
strain Thus, the mutant alleles, 28 and 42, are
reces-sive for sorbate growth, and a heterozygous
wild-type⁄ war1D strain did not show any haplo-insufficiency
phenotypes (Fig 2) However, when mutants 28 and
42 were crossed with the war1D strain, the diploid
strains remained hypersensitive to sorbate, and
dis-played the same growth behavior as the pdr12D
control strain These data suggest that the mutants
isolated in the UV mutagenesis screen were allelic to
WAR1 Thus, the mutant alleles were named War1-28
and 42, respectively Interestingly, diploid
War1-28⁄ War1-42 cells were more resistant than war1D ⁄
mutant diploids, suggesting a possible
cross-comple-mentation of mutant alleles, and implying that War1p
acts as a dimer [15]
Identification of the mutations in war1
To identify the actual mutations leading to the
loss-of-function phenotypes, the defective war1 alleles were
amplified by PCR from genomic DNA obtained from
the mutant strains and subjected to DNA sequencing
Sequencing of both DNA strands of War1-28
identi-fied an A to T mutation at position 1286, and a
change of C to T at position 1288, the latter
introdu-cing a translational stop codon (Fig 3) At the
amino-acid level, these mutations resulted in a N429I residue
exchange, and the nonsense mutation leads to
trun-cated War1-28p protein (Fig 3A) For the mutant
War1-42 allele, four clustered mutations were found: deletion of A2286, T2287 and T2288, and the G2291T transversion These four mutations caused three amino acid changes, namely K762N, F763M and the R764D deletion The rest of the protein remained unchanged
As depicted in the cartoon (Fig 3A), War1p is repre-sentative of the binuclear Zn(II)2Cys6 transcription factor family, all members of which contain a DNA-binding zinc finger at their N-terminus (amino acids 75–111), followed by two predicted nuclear localization signals (NLS amino acids 106–123 and 286–303), and
a coiled-coil domain mediating protein–protein interac-tions The putative transcriptional activation domain is located near the C-terminus, residues 911–937 Hence,
a loss-of-function phenotype of War1-28 may easily be explained by the absence of the activation domain, whereas the effect of the mutations in War1-42 on War1p function is not immediately obvious
Characterization of War1-42p and its post-translational modification
To determine if the mutant proteins are properly expressed, we epitope-tagged both War1-28p and War1-42p at the C-terminus by genomic integration of
a triple 3HA epitope, creating the strains YBB30 and YBB31, respectively Immunoblotting of protein extracts from exponentially growing cultures revealed that both mutant proteins displayed a mobility corres-ponding to their predicted molecular mass (Fig 3B) However, when compared with the wild-type, the steady-state concentrations of mutant War1-42p-3HA appeared to be markedly reduced Notably, the con-centrations of the truncated War1-28p-3HA appeared slightly increased, implying that the stability of the protein is affected by the different mutations
To address this point, we performed cycloheximide chase experiments The strains, YAK111, YBB30 and YBB31, were grown in YPD to an A600 of 1; then cycloheximide was added to block protein synthesis, and samples were collected at the indicated time points for immunoblotting (Fig 3C) The results show that the wild-type protein was quite stable, with a half-life
of 100–120 min Likewise, War1-28p-3HA was detect-able throughout the whole chase period (Fig 3C) In contrast, War1-42p-3HA displayed a much faster pro-teolytic turnover, as it was already below the detection limit 40 min after cycloheximide addition (Fig 3C) Thus, the low steady-state concentrations of War1-42p-3HA may be explained by its reduced stability Notably, sorbate failed to influence War1p stability, as the half-life was unchanged under stress (data not shown)
WT/WT
WT/war1Δ
WT/28
WT/42
war1Δ/28
war1Δ/42
28/42
pdr12Δ
YPD pH 4.5
control
+ Sorbate
Fig 2 The sorbate-sensitive mutants carry loss-of-function alleles
of WAR1 The strains W303-D (WT ⁄ WT), YBB21 (WT ⁄ war1D),
YBB24 (WT⁄ 28), YBB22 (WT ⁄ 42), YBB25 (war1D ⁄ 28), YBB26
(war1D ⁄ 42), YBB23 (28 ⁄ 42) and YBB14 (pdr12D) were grown to an
A600of 1, diluted to A600of 0.2 and spotted on to YPD, pH 4.5,
agar plates containing the indicated sorbate concentrations along
with three 1 : 10 serial dilutions Colony growth was inspected
after 48 h at 30 C.
Trang 5Stress-induced phosphorylation is absent
in War1-42p
Whereas for War1-28p the inability to induce PDR12
transcription was attributable to the lack of the
activa-tion domain, the explanaactiva-tion was not obvious for
War1-42p Notably, we have previously shown that
PDR12 induction coincides with War1p
phosphoryla-tion [15] Therefore, we determined the
post-transla-tional modification status of War1-42p-3HA under
both stressed and nonstressed conditions using
immu-noblotting (Fig 3D) The cultures were grown to an
A600of 1, split, and one half was treated with 8 mm
sorbate After 30 min, cells were harvested, and protein
extracts prepared and subjected to immunoblotting As
reported previously [15], wild-type War1p migrated as
a double band in unstressed cells and shifted to slower mobility forms upon sorbate addition (Fig 3D) In contrast, no mobility shift was detectable for War1-42p-3HA, as it migrated as a single band under both stressed and nonstressed conditions (Fig 3D) There-fore, the post-translational modification pattern of War1p, which is intimately linked to PDR12 stress induction, is absent in the War1-42p-3HA mutant, indi-cating that phosphorylation may be an essential step
in War1p activation Remarkably, War1-42p-3HA from unstressed cells exhibited a faster mobility on SDS⁄ polyacrylamide gels than authentic War1p (Fig 3D), suggesting that the basal modification in the absence of stress was also affected in War1-42p-3HA
Functional analysis of single-residue changes, K762N, F763M and R764D
The War1-42 allele contains a cluster of four muta-tions, leading to three residue changes To address which mutation alone or in combination with another one causes the phenotype, we constructed the CEN-based plasmids pCGWAR1-K762N, pCGWAR1-F763M and pCGWAR1-R764D carrying the single mutations, respectively Each of the three plasmids expressed a mutated version War1p with only one of three residue changes of War1-42p To determine the phosphorylation status of K762N,
War1p-war1-28
N429I STOP
war1-42
K762N F763M R764Δ Zn
NLS
AD
NLS
A
WT-3HA 28-3HA 42-3HA WT
loading control
cross reaction
B
War1p-3HA
War1-28p-3HA
War1p-3HA War1-28p-3HA War1-42p-3HA
0 20 40 60 80 100 120 min CHX
C
WT-3HA WT-3HA 42-3HA
D
unstressed + 8 mM sorbate
30 min
War1p-3HA
Fig 3 Organization, expression, stability and modification of War1p variants (A) The cartoon depicts the localization of mutations in the WAR1 gene abrogating its function as a specific Pdr12p regulator.
Zn, zinc finger; AD, activation domain Cartoon not drawn to scale (B) Expression and stability of the wild-type and mutant War1p vari-ants Cultures of the strains YAK111 (WT-3HA), YBB31 (28-3HA), YBB30 (42-3HA) and YPH499 (WT) were grown in YPD to an A 600
of 1 and harvested Yeast crude protein extracts equivalent to 1
A600were separated by PAGE (10% gel) and analyzed by immuno-blotting using the 12CA5 HA antibody Cross-reactions to the HA antibody served as a loading control (C) The strains YAK111 (War1p-3HA), YBB31 (War1-28p-3HA) and YBB30 (War1-42p-3HA) were grown in YPD to an A 600 of 1, then cycloheximide (CHX) was added to a final concentration of 0.1 mgÆmL)1, and samples were taken at the indicated time points Extracts (0.5 A600 for War1p-3HA and War1-28p-3HA, 1.5 A 600 for War1-42p-3HA) were fractionated by SDS ⁄ PAGE (10% gel), followed by immunodetec-tion of the War1p-3HA and variants by monoclonal 12CA5 HA anti-body (D) The strains YAK111 (WT-3HA), YBB30 (42-3HA) and YPH499 (WT) were grown in YPD to an A 600 of 1, then the cul-tures were split, and one half was treated with 8 m M sorbate for
30 min Crude cell extracts (equivalent to 1.5 A600for 42-HA and 0.5 A 600 for WT-HA and WT) were separated by SDS ⁄ PAGE (7% gel) and immunodetected using the monoclonal 12CA5 HA anti-body.
Trang 6F763M and War1p-R764D, as well as their ability to
induce Pdr12p expression, we performed
immuno-blotting under stressed and nonstressed conditions
(Fig 4A) Cultures of the war1D strain YAK120,
harboring pCGWAR1-K762N, pCGWAR1-F763M,
pCGWAR1-R764D or the control plasmid expressing
wild-type WAR1, were grown to an A600 of 1 The
cultures were split in half; one half was treated with
8 mm sorbate for 30 min, and the other left unstressed
Cells were then harvested, and protein extracts were
prepared and subjected to immunoblotting Whereas
War1p-F763M behaved as the wild-type War1p under
unstressed conditions, War1p-K762N showed a slightly
different modification pattern in unstressed cells In
contrast with wild-type War1p, which migrated as a
double band under nonstressed conditions, the
lower-migrating band was hardly detectable in War1p-K762N
(Fig 4A) However, sorbate shifted both
War1p-K762N and War1p-F763M to a slower mobility, as
was also observed for the wild-type control In
con-trast, War1p-R764D remained unmodified in response
to sorbate stress The mobility shift in response to
stress is tightly linked to PDR12 induction, which was
absent in the strain expressing War1p-R764D (Fig 4A)
In contrast, strains expressing the mutants
War1p-K762N and War1p-F763M showed greatly increased
Pdr12p concentrations in both the absence and
pres-ence of weak-acid stress Addition of sorbate did not
further increase Pdr12p expression levels (Fig 4A),
demonstrating that the K762N and
War1p-F763M single mutants are gain-of-function variants
However, their hyperactivity is suppressed by the
pres-ence of the additional R764D deletion in War1-42p
Furthermore, we tested the strains expressing the
mutant War1p variants for their ability to grow on
YPD, pH 4.5, in the presence or absence of different
sorbate concentrations (Fig 4B) Consistent with the
immunoblotting data, the War1p-R764D strain was as
hypersensitive to sorbate as the war1D control because
of the inability to induce Pdr12p, whereas
War1p-K762N and War1p-F763M showed normal growth
when compared with wild-type cells (Fig 4B)
Nota-bly, the hyperactivity of K762N and
War1p-F763M variants failed to cause hyper-resistance to
weak organic acids (data not shown)
Because War1-42p displayed reduced protein
stabil-ity (Fig 3C), cycloheximide chase experiments were
also performed with the War1p-R764D single mutant
exactly as described above for War1-42p (Fig 3C)
Detection of the different War1p variants
demonstra-ted a markedly reduced stability of War1p-R764D
compared with wild-type, although protein
concentra-tions did not decrease as fast as for War1-42p
F763M
War1p
Pdr12p
Pdr5p
WTwar1
Δ
K762N F763MR764
Δ
YPD pH 4.5
+ 0.5 m M sorbate + 1 m M sorbate + 2 m M sorbate
War1p
War1p-R764Δ
War1-42p
B A
C
Fig 4 War1p-764D causes sorbate hypersensitivity and fails to induce Pdr12p (A) Cultures of YAK120 cells were transformed with pCGWAR1, K762N, F763M or pCGWAR1-R764D and grown in YPD to an A 600 of 1; cultures were split in half, and one half was treated with 8 m M sorbate for 30 min, while the other remained untreated Crude cell extracts (0.5 A 600 ) were separated by SDS ⁄ PAGE (7% gel), and immunodetected using polyclonal antibodies against War1p, Pdr12p and Pdr5p (B) YAK120 was transformed with pCGWAR1, K762N, pCGWAR1-F763M or pCGWAR1-R764D and grown to an A 600 of 1, diluted to
A600¼ 0.2, 0.02 and 0.002; culture aliquots were spotted on to YPD, pH 4.5, agar plates containing sorbate concentrations as indi-cated Colony growth was inspected after 48 h at 30 C (C) The strain YAK120 transformed with pCGWAR1 or pCGWAR1-R764D and strain YCS42-D4 (War1-42p) were grown in YPD to an A600of
1 Cycloheximide (CHX) was added at a final concentration of 0.1 mgÆmL)1; samples were taken at the indicated time points Cell-free extracts (0.5 A600for War1p, 1.0 A600for War1-42p and War1-R764Dp) were separated by SDS ⁄ PAGE (7% gel) and trans-ferred to nitrocellulose membranes War1p and variants were detected by immunoblotting using polyclonal antibodies to War1p.
Trang 7(Fig 4C) This may indicate that the cluster of three
residue changes in War1-42p, as well as single residue
changes, even if two of them lead to a
gain-of-func-tion, change War1p folding, thereby destabilizing
War1p more than the loss of a single amino acid as in
War1-R764Dp
War1-42p localizes to the nucleus but is unable
to bind to the WARE in vivo
We have previously demonstrated that War1p is a
nuc-lear protein [15] Although the mutational changes in
War1-42p left the DNA-binding domain and both NLS
unaffected, we wanted to test whether War1-42p is also
properly localized to the nucleus Hence, we carried out
fractionation experiments using purified nuclear
frac-tions from various strains Subcellular fracfrac-tions were
isolated by following a gentle cell lysis procedure to
preserve nuclear integrity, and subjected to
immuno-blotting using polyclonal antibodies specific for War1p,
the nuclear marker protein Swi6p and the cytoplasmic
hexokinase Hxk1p (Fig 5A) As shown in Fig 5A,
War1-42p, like the wild-type control War1p, localized
to the nucleus in the steady state As expected, Hxk1p
was predominantly found in the soluble cytoplasmic
fraction The signal for Hxk1p in the nuclear fraction is
due to normal unavoidable contamination of the
lear fraction with cytosolic proteins However, the
nuc-lear marker, Swi6p, entirely cofractionated with both
War1-42p and wild-type War1p (Fig 5A),
demonstra-ting that the normal nuclear localization of War1-42p
is unaffected by the mutations No immunoreactive
material was detectable in war1D cells, confirming the
specificity of the polyclonal anti-War1p serum
Nota-bly, the polyclonal antibodies also detected a War1p
degradation product (Fig 5A), which was not
recog-nized by the monoclonal HA antibody (Fig 3) Hence,
the lack of function in War1-42p is probably a
conse-quence of impaired activation or direct binding to the
WARE rather than aberrant cellular localization
War1-42 strains cannot tolerate sorbate, suggesting
that they may lack the capacity for proper modification
of War1p under stress conditions To exclude this
pos-sibility, we introduced War1-42p into a wild-type
back-ground to obtain strain YBB32 With this strain
carrying one wild-type and one mutated allele of
WAR1, we repeated the stress experiments described
above and checked for the mobility of War1-42p by
immunoblot analysis Even in the presence of wild-type
War1p and a normal stress response, War1-42p
remains unmodified (data not shown), suggesting that
the mutations prevent normal modification of the
transcription factor rather than indirect effects, which
3 2 1
1+2 1+3 2+3
WT
war1-42 war1Δ
WT war1-42 war1
Δ
*
*
42
C N S C S
C N
War1p
Swi6p
Hxk1p
B A
Fig 5 Nuclear War1-42p is unable to decorate the PDR12 promoter
in vivo (A) Subcellular fractions were prepared from wild-type cells (WT), War1-42 mutants (42) and cells lacking War1p (war1D) as des-cribed in Experimental procedures About 2 A 600 equivalents were subjected to immunoblotting using polyclonal antibodies against War1p, Swi6p and Hxk1p S, Total input; N, nuclear pellet; C, cyto-plasmic fraction (B) YPH499 wild-type (WT), YAK110 (war1D) and YCS42-D4 (War1-42) cells were grown to the early exponential growth phase and treated with dimethyl sulfoxide to methylate DNA For in vivo footprinting, chromosomal DNA was prepared and used as a template for primer extension with a labeled oligonucleo-tide primer corresponding to )497 to )472 of the PDR12 promoter The reaction mixture was resolved through a sequencing gel, exposed to a phosphoimaging screen, and signals were quantified Intensities of traces are compared in the indicated combinations An asterisk marks a protected G ( )631) in the War1-42 allele Differ-ences are indicated by bars for deprotected G residues ( )643, )642, )617, )618) and aligned with the sequence of the region.
Trang 8would be a consequence of the impaired growth of
War1-42mutants under stress
Because nuclear localization of War1-42p was
unaf-fected, we determined whether War1-42p still binds to
the WARE in the PDR12 promoter To clarify this,
we performed in vivo footprinting experiments in cells
expressing War1-42p The strains YPH499 (wild-type),
YAK110 (war1D) and YCS42-D4 (War1-42) were
cul-tivated to the exponential growth phase and then
trea-ted with dimethyl sulfoxide to methylate guanines and
to some extent adenines in the genomic DNA
Chro-mosomal DNA was isolated, and the methylation
status was determined by primer extension analysis
(Fig 5B) Comparison of the methylation patterns of
the different strains revealed that the mutant War1-42
and war1D exhibit almost identical patterns (Fig 5B,
2+3) In contrast, when both were compared with the
wild-type (Fig 5B, 1+2 and 1+3), deprotection at the
same nucleotides (black bars) was observed These
results clearly indicate that War1-42p is unable to
dec-orate the WARE in the PDR12 promoter in vivo,
nicely explaining the loss-of-function phenotype and
the sorbate hypersensitivity of War1-42 mutant cells
Taken together, our genetic screen identified two
muta-tions in the putative MHR region of the War1p
tran-scriptional regulator, suggesting that the MHR is
essential for War1p function Mutations in the MHR
may cause structural changes that impair
post-transla-tional phosphorylation, affecting DNA binding of
War1p or the recruitment of other as yet unknown
coregulators
Discussion
We are interested in dissecting the response pathway
necessary for cellular adaptation to stress from weak
organic acids in the yeast, S cerevisiae Using a
func-tional genomic approach, we have identified the
War1p regulator as the dedicated transcription factor
required for Pdr12p induction following weak-acid
stress exposure [15] In this study, we report the
iso-lation and characterization of two loss-of-function
war1 alleles that give rise to War1p variants that are
unable to mediate Pdr12p induction in response to
sorbate stress We exploited a classical genetic screen,
taking advantage of a lacZ reporter driven by the
PDR12promoter, which otherwise controls expression
of the Pdr12p weak-acid anion-efflux pump [7] After
UV mutagenesis, we screened more than 10 genome
equivalents of mutant colonies for their capacity in
PDR12 induction We expected to isolate mutants in
membrane sensors, signaling components such as
kinases, phosphatases and perhaps transcriptional
regulators However, most remarkably, only two yeast mutants were isolated in which sorbate-mediated induction of Pdr12p was completely abolished (Fig 1A) The weak-acid hypersensitivity of both mutant strains was attributed to mutations in the WAR1 gene (Fig 3) DNA sequencing identified the mutations in the nonfunctional war1 alleles Whereas War1-28encoded a truncated regulator which was due
to a stop codon, War1-42 carried three residue chan-ges close to the C-terminus Hence, the genetic approach yielded only mutant variants of the War1p regulator, suggesting that War1p is the major and per-haps only stress regulator of Pdr12p
The genetic approach confirms our strategy of using functional genomics which led to the identifica-tion of War1p Nevertheless the genetics data allow several interpretations about the function of War1p Firstly, none of the signaling components except War1p, including the War1p kinase(s), appear to be essential, perhaps because of redundant functions in the pathway Secondly, Pdr12p and War1p represent the key elements of the response pathway and there are no other essential components Thirdly, we can-not entirely exclude the possibility that other mutants have been missed by the low amount of sorbate used for the PDR12 promoter induction screen because of weak-acid hypersensitivity How-ever, as Pdr12p is the major determinant of weak-acid resistance, and the main target of War1p [32],
we reason that defects in genes encoding components acting upstream of War1p should not display higher sorbate sensitivities than nonfunctional War1p vari-ants themselves
The sorbate hypersensitivity phenotype of War1-28 cells can easily be explained, because this allele carries
a nonsense mutation leading to a truncated War1-28p (Fig 3A) Hence War1-28p lacks the C-terminal acti-vation domain, which is necessary for transcriptional activation of the target genes by other Zn(II)2Cys6 transcription factors [33] Notably, the truncated War1-28p protein, although expressed at higher levels than the wild-type, does not interfere with the function
of authentic War1p in diploid cells (Fig 2), which might be a direct consequence of impaired dimer for-mation of War1p or a lack of DNA binding Indeed,
in the case of War1-42p, in vivo footprinting data (Fig 5) indicate an inability to bind to the WARE, which is normally decorated by wild-type War1p in the presence or absence of the stress agent [15] Thus, the lack of PDR12 stress induction by War1-42p is per-haps due to its inability to bind to the promoter WARE of its target gene Alternatively, the mutations may also reduce the binding affinity of the War1-42p,
Trang 9thereby causing impaired assembly of the active
tran-scription complex
A lack of DNA binding by War1-42p may be
explained in several ways First, immunoblotting
cycloheximide chase experiments indicated that
War1-42p shows lower steady-state protein concentrations
and decreased stability compared with the wild-type
War1p (Fig 4) Hence, the amount of protein might
simply be too low to allow binding to the target DNA
Secondly, the mutations may reduce affinity for
WARE binding or prevent the formation of War1p
dimers, which appears necessary for War1p function
[15] Thirdly, reduced protein concentrations may still
allow WARE binding, but other determinants are
pre-venting the DNA recognition Although band shift
experiments using glutathione S-transferase
(GST)-War1p suggested that WARE binding does not require
additional factors or modifications [15], this may not
entirely reflect the situation in vivo As shown for
Gal4p, the prototype zinc cluster transcription factor,
its DNA-binding properties can be different in vitro
and in vivo and may involve sequences in the
regula-tory domains distinct from the zinc finger or even
additional factors [34] Therefore, the war1 mutations
identified perhaps destroy structural features necessary
for the interaction with accessory proteins involved in
target site recognition, WARE binding or
post-transla-tional modification of War1p
Genetic separation of the clustered mutations in
War1-42p revealed that R764D displays a complete
loss-of-function phenotype In sharp contrast,
how-ever, the residue changes, K762N and F763M, lead to
constitutive War1p hyperactivity (Fig 4A) Strikingly,
War1p-R764D is no longer phosphorylated in response
to sorbate challenge Conversely, War1p-K762N and
War1p-F763M are phosphorylated upon stress,
although they are already active in the absence of
sorbate stress (Fig 4A) Therefore, in constitutively
active War1p variants, sorbate stress is tightly linked
to phosphorylation, even if the protein is already
acti-vated War1-42p is functionally inactive and also not
phosphorylated in response to weak-acid treatment
(Fig 3D) Hence, the R764D mutation can be
consid-ered dominant for War1p loss-of-function when
pre-sent in combination with the hyper-activating
mutations, K762N and F763M
The basal modification status of War1-42p is
differ-ent from wild-type War1p, as they display distinct
mobilities on immunoblotting DNA binding in vivo
may well require basal post-translational modifications,
as present in wild-type War1p but absent in the
mutant variant (Fig 3D) These modifications either
directly influence the DNA-binding capability or are
necessary for the interaction with another as yet unknown cofactor that would facilitate binding to the PDR12promoter
The fact that loss-of- function mutations reside out-side the zinc finger or the NLS suggests an altered conformation or structure This is consistent with the apparent absence of stress-induced phosphorylation in War1p-R764D and its reduced protein stability Thus, only massive folding changes can explain the inactiv-ity of War1p-R764D, which may hinder phosphoryla-tion Mutations may also affect the structure of confined domains such as the MHR rather than the whole tertiary structure Hence, the lack of phos-phorylation is most likely a consequence of massively altered War1p conformation rather than altered struc-ture of the kinase targets themselves Further, the residue changes in War1-42p do not involve serine, threonine, tyrosine or histidine (Fig 3A) In any case, the nonphosphorylated war1 alleles are nonfunctional, indicating that certain post-translational modifications are essential for War1p to induce transcription of PDR12 upon stress
From the homologies between zinc finger regulators,
a defined MHR [33] is not immediately apparent in War1p However, it seems plausible that the stretch carrying the residue changes is functionally similar to the MHR Because the K762N and War1p-F763M mutants in this stretch are constitutively active, the MHR of War1p is likely to play a major role in the regulation of its transcriptional activity, as well as
in the specificity of target site recognition If the regu-lator is present in limiting amounts, a reduced or altered specificity because of lack of a functional MHR will remove the protein from its binding sites
in vivo [33] However, we wish to provide another explanation for the loss-of-function in War1-42p The drastic decrease in the total amount of the transcrip-tional regulator in combination with a reduction in sequence recognition specificity may account for the observed lack of WARE binding by War1-42p Defect-ive nuclear localization can be excluded, because the NLSs are not affected by the mutations, and because the mutant proteins display proper nuclear localiza-tion Another possibility is that War1-42p binds to WARE with much lower affinity, insufficient to be detected by in vivo footprinting (Fig 5B)
Thus, more information about the structure and potential interaction partners of War1p is required For instance, the War1-42 mutant can be used as a tool to identify intragenic suppressor mutations Furthermore, high-copy or second-site suppressors may lead to the identification of unknown War1p-interacting partners This seems to be a feasible and promising approach
Trang 10considering the suppression of the constitutive activity
of K762N and F763M by an additional R764D
dele-tion Finally, the War1-42 mutant allele should be
use-ful as a tool for learning more about the molecular
structure, as well as the protein–protein and protein–
DNA interactions, of this binuclear zinc transcriptional
regulator The polyclonal antibodies to War1p should
be useful in identifying the upstream components of the
response pathway, including War1p-specific kinases
and phosphatases implicated in the modulation of
War1p activity during adaptation to stress induced by
weak organic acids
Experimental procedures
Yeast strains, growth conditions, and growth
inhibition assays
Rich medium (YPD) and synthetic medium were prepared
essentially as described elsewhere [35] Unless otherwise
indicated, all yeast strains were grown routinely at 30C
S cerevisiaestrains used in this study are listed in Table 1
To determine weak-acid susceptibility, exponentially
grow-ing cultures were adjusted to A600of 0.2 and diluted 1 : 10,
1 : 100 and 1 : 1000 Equal volumes of these serial dilutions were spotted on to YPD, pH 4.5, plates containing the indi-cated sorbate concentrations exactly as previously described [15]
Gene disruptions and strain constructions
The deletion of WAR1 was performed by a PCR-based method using the disruption cassette of the plasmid pFA6a-HIS3MX6 [36] The PDR12 gene was disrupted with a hisG-URA3-hisG cassette from the plasmid pYM63 [7] For epitope tagging of the wild-type or mutant versions of WAR1, the triple HA tag or GFP tag was amplified from plasmids pFA6a-3HA-KANMX6 or pFA6a-3HA-HIS3MX6 [37] using appropriate primers, followed by integration at the genomic locus
For the PDR12prom-lacZ reporter construct used in the UV-mutagenesis screen, we amplified the PDR12 promoter
by PCR, introducing an EcoRV site at position)1168 and
a HindIII site at position +8 The EcoRV–HindIII frag-ment was then cloned into the vector YIp357 [38], yielding plasmid pCS12Z-I The correct sequence of the insert was verified by DNA sequencing To construct the strain carry-ing lacZ under the control of the PDR12 promoter, plasmid
Table 1 Yeast strains used in this study.
W303–1B MATa ura3-1 leu2-3112 his3-11,15 trp1-1 ade2-1 can1-100
(W303-1A - MATa, W303-D - MATa ⁄ a)
[45]
YBB22 MATa⁄ a ura3-1 leu2-3112 trp1-1 ade2-1 can1-100 ura3-52::pCS12ZI
URA3 leu2-D1 his3-D200 trp1-D1 ade2-10 oc lys2-801 a War1-42
This study YBB23 MATa⁄ a ura3-1::pCS12ZI URA3 LEU2 his3-11,15 trp1-1 ade2-1 can1-100
War1-28 ura3-52::pCS12ZI URA3 leu2-D HIS3 trp1-D1 ade2-10 oc lys2-801 a War1-42
This study YBB24 MATa⁄ a ura3-1::pCS12ZI URA3 LEU2 HIS3 trp1-1 ade2-1 can1-100 War1-28
(isogenic to W303-D)
This study YBB25 MATa⁄ a ura3-1::pCS12ZI URA3 LEU2 his3-11,15 trp1-1 ade2-1 can1-100 War1-28
war1D::HIS3MX6 (isogenic to W303-D)
This study YBB26 MATa⁄ a ura3-1 leu2-3112 his3-11,15 trp1-1 ade2-1 can1-100 war1D::HIS3MX6 This study
ura3-52::pCS12ZI URA3 leu2-D1 his3-D200 trp1-D1 ade2-10 oc lys2-801a War1-42 YBB30 MATa ura3-52::pCS12ZI URA3 War1-42-3HA HIS3MX6 (isogenic to YPH499) This study YBB31 MATa ura3-1::pCS12ZI URA3 LEU2 War1-28-3HA HIS3MX6 (isogenic to W303-1B) This study YBB32 MATa⁄ a ura3-1 LEU2 his3-11,15 trp1-1 ade2-1 can1-100 ura3-52::pCS12ZI URA3
leu2-D1 his3-D200 trp1-D1 ade2-10oclys2-801a War1-42-3-HAHIS3MX6
This study