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J. Biol. Chem., Vol. 276, Issue 43, 40254-40262, October 26, 2001
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§,
From the
Johnson Research Foundation and Department
of Biochemistry and Biophysics, University of Pennsylvania School of
Medicine, Philadelphia, Pennsylvania 19104 and the ¶ Department of
Molecular and Cell Biology, University of California,
Berkeley, California 94720
Received for publication, July 5, 2001, and in revised form, August 16, 2001
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ABSTRACT |
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The expression of heat shock proteins in response
to cellular stresses is dependent on the activity of the heat shock
transcription factor (HSF). In yeast, HSF is constitutively bound to
DNA; however, the mitigation of negative regulation in response to
stress dramatically increases transcriptional activity. Through
alanine-scanning mutagenesis of the surface residues of the DNA-binding
domain, we have identified a large number of mutants with increased
transcriptional activity. Six of the strongest mutations were selected
for detailed study. Our studies suggest that the DNA-binding domain is
involved in the negative regulation of both the N-terminal and
C-terminal activation domains of HSF. These mutations do not
significantly affect DNA binding. Circular dichroism analysis suggests
that a subset of the mutants may have altered secondary structure, whereas a different subset has decreased thermal stability. Our findings suggest that the regulation of HSF transcriptional activity (under both constitutive and stressed conditions) may be partially dependent on the local topology of the DNA-binding domain. In addition,
the DNA-binding domain may mediate key interactions with ancillary
factors and/or other intramolecular regulatory regions in order
to modulate the complex regulation of HSF's transcriptional activity.
All cells respond to stresses, such as elevated
temperatures and other changes in cellular conditions, by increasing
the expression of heat shock proteins, a set of proteins that protect
the cell from damage caused by stress and also aid the cell's recovery after the removal of stress. In eukaryotes, the increased expression of
heat shock proteins is regulated by the heat shock transcription factor
(HSF).1 HSF binds to a
conserved DNA sequence called a heat shock element (HSE), which is
defined as a series of alternating, inverted repeats of the conserved
sequence NGAAN (1, 2). HSEs range in size from two to more than six
repeats, and all heat shock promoters have at least one three-repeat
HSE or two proximal two-repeat HSEs. The two-repeat HSEs can be
arranged in either a head-to-head (NGAANNTTCN) or tail-to-tail
(NTTCNNGAAN) orientation. The strength of HSF's activation depends
primarily on the number of HSEs within the promoter and secondarily on
the sequence of the non-conserved "N" residues and the orientation
of the binding site.
Budding yeast, such as Saccharomyces cerevisiae, have only a
single HSF, which is an essential gene that has a constitutive function
(3, 4). Under all cellular conditions, yeast HSF appears to be
localized in the nucleus in a DNA-binding competent form (5, 6). Key to
the function of yeast HSF is the fact that it has different levels of
transcriptional activity in response to different cellular conditions.
Under constitutive or normal growth conditions, yeast HSF has a low
level of transcriptional activity, which can vary 10-fold between
growth at 15 and 30 °C (3). After heat shock or stress, yeast HSF
acquires a high level of transcriptional activity, which can be up to
200-fold greater after a transient 30-min heat shock at 39 °C (3).
This increased level diminishes rapidly once the transient stress is removed. If cells are shocked and maintained at the heat shock temperature for several hours, there is an early peak of activity, which then readjusts to a basal level that is significantly higher than
the level prior to the increase in temperature (7). Jakobsen and
colleagues (8) have shown that yeast heat shock activation responds to
a change in temperature, rather than an absolute temperature.
There are at least four clearly defined domains for the S. cerevisiae gene HSF1 (Fig. 1). The central core,
responsible for DNA binding and oligomerization, has been highly
conserved in all HSFs. The trimerization domain consists of a
three-stranded coiled-coil (9-11). The DNA-binding domain is a
variation of the winged-helix-turn-helix motif (12), with an unusual
The regulation of yeast HSF's activity occurs at many levels, although
it appears to function primarily through negative regulation of HSF's
activity in the absence of stress. The level and extent of yeast HSF's
phosphorylation is dependent on cellular conditions (3); therefore, it
is likely that protein kinases and phosphatases are involved in
regulating HSF's activity. Studies on HSF from Kluyveromyces
lactis, which is closely related to S. cerevisiae, have
shown that phosphorylation is likely involved in repressing HSF's
activity after stress is removed (18). Several studies have shown that
heat shock proteins help to repress mammalian HSF's activity after the
removal of stress (19, 20), although it is not clear whether this is
the case in yeast (8, 21).
At least four cis-acting regions of yeast HSF have been identified as
important in the regulation of its activity. In particular, they are
involved in restraint of HSF's activity in the absence of stress, as
their deletion causes an increase in HSF's constitutive activity,
suggesting that these regions function as negative regulators by
masking the activation domains. This negative regulation could occur
through intermolecular interactions with other proteins or through
intramolecular interactions between these cis-acting regions and the
activation domains.
The four cis-acting regions include N-terminal and C-terminal
regulatory regions, as well as the DNA-binding and trimerization domains (Fig. 1). Deletion of the
N-terminal regulatory region, located between residues 40 and 170, results in a total removal of the negative regulation of the C-terminal
activation domain, such that HSF has the same high level of activity
before and after stress (7, 22). Deletion or mutation of the CE2
regulatory region, located between residues 532 and 552 and including a
short C-terminal hydrophobic heptad repeat and several critical serine residues, also results in HSF with an increased constitutive activity (18, 22, 23). Because the CE2 regulatory region is involved in the
sustained, rather than the transient heat shock response, it is likely
regulating the C-terminal activation domain, rather than the N-terminal
activation domain (18), although no definitive studies have been
reported to support this.
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INTRODUCTION
TOP
ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
REFERENCES
-helical bulge and proline-centered kink combination in its second
helix (i.e. the first helix of the helix-turn-helix motif)
(13, 14). There are two activation domains, located at the N and C
termini of the protein. The N-terminal activation domain is found
within the first 170 amino acids (7, 15), with the most potent part of
the activation domain within the first 66 amino
acids.2 The C-terminal
activation domain is located between residues 595 and 783 (7, 15, 16).
The activation domains appear to play different roles, with the
N-terminal activation domain responsible for the initial transient
increase in activity in response to stress and the C-terminal
activation domain responsible for the more sustained stress response
(7). Nevertheless, either activation domain can be deleted
without affecting viability at constitutive (i.e. non-heat
shock) temperatures (7, 15). Deletion of the C-terminal activation
domain results in a temperature-sensitive phenotype, emphasizing its
role in the ability of yeast to thrive at higher growth temperatures.
In addition, the C-terminal activation domain is critical for the
heat-induced or glucose starvation-induced increase of
expression of the metallothionein gene CUP1,
a non-canonical heat shock gene, but not for the heat-induced
increase of expression of SSA1 and
SSA3, two of the yeast Hsp70 homologues (17).
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Fig. 1.
Schematic diagram of full-length HSF from
S. cerevisiae. AD, activation domain;
RR, regulatory region.
The central core, which encompasses the DNA-binding and trimerization
domains, is also involved in repressing transcriptional activity (15).
Studies on a series of fusions between fragments of HSF and a
heterologous DNA-binding domain have shown that removal of the central
core increases HSF's transcriptional activity (15). Furthermore,
several studies have shown that point mutations within either the
DNA-binding or trimerization domains cause an increase in constitutive
and/or induced transcriptional activity (13, 14, 16, 22, 24). The
DNA-binding domain mutations include M232V, identified as increasing
the activity of a heterologous VP16 transcriptional activation domain,
and R206S, identified as one of two mutations within HSF responsible
for high basal transcription of the metallothionein gene
CUP1, known to be regulated by HSF. In addition, a detailed
study of the bulged-kinked second helix of the DNA-binding domain
showed that it was critical for transcriptional activity; removal of
the
-helical bulge through single amino acid deletions causes an
increase in transcriptional activity that might be related to thermal
destabilization of the DNA-binding domain (13). Substitution of the
conserved proline, which is located at the center of the kink, by a
lysine (though not alanine) causes an increase in transcriptional
activity (14). None of these studies looked systematically at how these
domains influenced activity, nor did they analyze whether the central core has differential regulation of the two activation domains.
In order to explore further the role of the DNA-binding domain in
regulating transcriptional activity, we have studied the transcriptional activity of a series of alanine-scanning mutants that
cover the surface of the DNA-binding domain (12, 25). The majority of
the surface residue mutations cause a change in transcriptional
activity compared with wild-type HSF. Of these, only a small number
decrease transcriptional activity, whereas ~80% cause an increase in
transcriptional activity. By mapping the positions of these residues
onto the crystal structure of the DNA-binding domain, we can conclude
that multiple surfaces of the DNA-binding domain are involved in
regulation of transcriptional activity. We have focused on six of the
mutants with the largest increase in transcriptional activity. We
analyzed how the mutations affected the transcriptional phenotype in
the absence of one or other of the activation domains. Our results show
that the DNA-binding domain is involved in negative regulation of both
the N- and C-terminal activation domains. Intriguingly, we also found
that specific residues differentially affected the activity of the two
transcriptional activation domains. The ability of the DNA-binding
domain mutations to influence transcriptional activity does not appear
to be related to changes in DNA-binding affinity, but may be related,
in some cases, to changes in the thermal stability and/or structure of the domain. Models for how the DNA-binding domain influences negative regulation of transcriptional activity are discussed.
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EXPERIMENTAL PROCEDURES |
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Plasmids and Yeast Strains-- The DNA-binding domain mutants used for yeast expression were all constructed from pHN1002, a CEN/AR4S/TRP1 yeast shuttle vector carrying a full-length copy of the S. cerevisiae HSF1 gene expressed from its own promoter (25). Construction of the full-length versions of the alanine-scanning mutants has been described (25). C-terminal truncations of specific alanine-substitutions were based on pHN2256, a version of pHN1002 that includes the first 583 residues of HSF followed by valine and asparagine as cloning artifacts and then a stop codon (gift of E. E. Powers). The DNA-binding domain mutations were transferred from the full-length background into pHN2256 using unique BamHI and StyI sites. N-terminal truncations of specific alanine substitutions used the plasmid pHN2241, a version of pHN1002 in which residues 145-833 are expressed from the natural HSF1 promoter (gift of E. E. Powers). This plasmid was digested with NcoI (which was blunted by filling-in with DNA polymerase) and StyI; this creates a backbone that includes the HSF1 promoter and the last 440 residues of HSF. Plasmids containing the full-length HSF versions of the mutants were digested with BamHI (which was blunted by filling-in with DNA polymerase) and StyI; this creates a fragment of HSF containing residues from 67 to 393. Ligation of these restriction fragments with the digested pHN2241 resulted in plasmids that used the natural HSF1 promoter to express residues 67-833 of HSF, preceded by methionine and aspartate (cloning artifact) at the N terminus.
The yeast expression plasmids were all transformed into the tester
strain PS145 (gift of P. Sorger). This strain is a haploid derivative
of S. cerevisiae W303 (MATa ade2-1 trp1
can1-100 leu2, 3-112 his3-11, 15 ura3), which carries the
HSF1
2::LEU2 chromosomal disruption
and a wild-type HSF1 gene under the control of a
GAL1 promoter on a derivative of the
URA3-containing plasmid YCp50 (3); it can only grow when
galactose is present. The transformants were tested for their ability
to grown in the absence of galactose. Once it was confirmed that the
particular alanine-substituted HSF was sufficient to allow viability
(25), the transformant was cured of the pGAL1-HSF1
URA3-based plasmid by growth on 5-fluoroorotic acid and uracil
(26). The resultant cells were transformed with the plasmid pHSE2-lacZ,
a 2-µm URA3-based plasmid in which the lacZ
gene is driven by a synthetic heat shock promoter (6).
-Galactosidase Assays--
Single colonies from a fresh plate
were used to inoculate selective synthetic media. The cells were grown
at 30 °C for 15-18 h until the cells were in early log phase growth
(A600 ~ 0.3). To heat induce the cells, 5 ml
of culture were transferred into a warm culture tube and shaken in a
42 °C water bath for 30 min, followed by a recovery growth period in
a 30 °C shaking water bath for 90 min. For every strain with a
mutant HSF, two to five colonies were assayed with a non-induced and
induced culture for each colony.
There were some minor differences in the assays done for the original 58 full-length HSF mutants and the assays done later for the 6 HSF mutants with increased transcriptional activity. Because all of the 58 full-length HSF mutants could not be tested within a single day, care was taken to ensure reproducibility from day to day. As an additional control, at least two colonies with wild-type HSF were tested each day that the assay was performed. Each set of raw data from each mutant was compared with the entire set of data from all of the wild-type controls. In order to analyze the data, Student's t test assuming equal variance was used from the statistical package in Microsoft Excel. The significance value was set at 0.5.
For the six mutant HSFs, the assays were grouped according to the length of the HSF construct, i.e. HSF-(1-583), HSF-(66-833), or HSF-(1-833). Within a single day, all six mutants and wild-type HSF could be tested, and each set of mutants was tested over several days. Because HSF-(1-583) grows poorly, all three sets of these mutants were grown in selective synthetic media with 3% dextrose (compared with 2% dextrose found in standard recipes).
-Galactosidase activity was determined as described previously (6,
27). Briefly, crude yeast extract was prepared from 3-4.5 ml of cells,
which were resuspended in 200 µl of Z buffer (60 mM
Na2HPO4, 40 mM
NaH2PO4, 10 mM KCl, 1 mM MgSO4, 50 mM
-mercaptoethanol). 10 µl of 10% Triton X-100 and 200 µl of
acid-washed glass beads (425-600 µm, Sigma) was added, followed by a
10-min incubation on ice. The tubes were then vortexed for 10 min at
4 °C, and the cell debris was separated from the crude extract by a
10-min centrifugation. Total protein concentration was estimated using
a Bradford protein assay. For the assay, typically 100 µl (for the
non-induced cells) or 50 µl (for the induced cells) of crude cell
extract was added to Z buffer to a final volume of 500 µl. To start
the assay, 100 µl of 4 mg/ml ONPG (in 0.1 M
KPO4) was added and the tubes placed in a 28 °C water
bath. The reaction was stopped by raising the pH with the addition 250 µl of 1 M Na2CO3; this addition
was done either at the appearance of a yellow color or at a 4-h maximum time point. The amount of the cleavage produce was detected by absorbance at 420 nm. The activity was calculated as
(A420)/(t·v·p), where t is time in minutes, v is volume of
extract in microliters, and p is protein concentration in
mg/ml.
Western Blotting--
Cells were grown to saturation or to early
log phase. Typically, 1.5 ml (saturated cells) or 4.5 ml (log phase
cells) were pelleted and resuspended by vortexing in 200 µl of 2×
SDS-PAGE loading buffer (0.125 M Tris (pH 6.8), 4% SDS,
20% glycerol, 1%
-mercaptoethanol). The tubes were boiled for 5 min and incubated on ice for 5 min. Following addition of 100 µl of
acid-washed glass beads (425-600 µm, Sigma), the tubes were vortexed
for 10 min at 4 °C and boiled for 5 min, and then the cell debris
was separated from the crude extract by a 10-min centrifugation at 4 °C. The amount of crude extract was quantitated using the Pierce BCA assay. Equal amounts of protein were loaded onto an SDS-PAGE gel.
The gel was electroblotted overnight onto an Immobilon filter (Millipore), which was probed with one of two different rabbit anti-HSF
antibodies (gifts of P. Sorger and D. Gross). The blots were analyzed
either by a colorimetric assay (using a goat anti-rabbit alkaline
phosphatase conjugate) or by chemiluminescence (using a donkey
anti-rabbit horseradish peroxidase conjugate).
Overexpression and Purification of HSF Fragments Containing the DNA-binding and Trimerization Domains-- The expression plasmid pHN136, previously described as Sc-DT(73L) (28), is a derivative of pET-3b (29) and contains the coding sequence for S. cerevisiae HSF amino acid residues 171-424, which includes the DNA-binding and trimerization domains. Mutations in the DNA-binding domain were introduced into pHN136 by a megaprimer polymerase chain reaction mutagenesis approach and confirmed by DNA sequencing. The plasmids are named pHN484 (K178A), pHN485 (D185A), pHN487 (R206A), pHN488 (N222A), pHN489 (H236A), and pHN490 (K237A).
The pET-3b expression vectors were transformed into the
Escherichia coli strain BL21(DE3) (29) containing a
derivative of the plasmid pAcYc177 (30) that overexpresses
lac repressor. Cells were grown shaking at 37 °C in
Terrific Broth containing 50 µg/ml each ampicillin and kanamycin
until they reached an A600 of ~0.5. Cells were
induced by addition of
isopropyl-1-thio-
-D-galactopyranoside to 3.75 mM, grown for an additional 3 h, harvested by
centrifugation, and stored at
20 °C. The frozen pellets were
thawed and resuspended in an equal volume of 50 mM Tris (pH
7.0), 600 mM NaCl, 5 mM MgCl2, and
10% glycerol. Lysozyme was added to a final concentration of 0.1 mg/ml, and the cells were incubated by shaking at 4 °C for 1 h.
The cell suspension was sonicated, and the lysed cells were centrifuged
at 39,000 × g for 20 min at 10 °C. The high speed supernatant was precipitated by addition of saturated ammonium sulfate
to a final concentration of 18%. The mixture was centrifuged at
39,000 × g for 20 min at 10 °C. The supernatant was
removed and the pellet resuspended in a minimal volume of 50 mM HEPES (pH 8.0), and 600 mM NaCl. All column
chromatography was conducted on an Amersham Pharmacia Biotech AKTA
Prime chromatography system at 4 °C, with absorbance and
conductivity monitored simultaneously. The resuspended pellet was
loaded onto a HiPrep 16/10 butyl column (Amersham Pharmacia Biotech)
equilibrated in 50 mM HEPES (pH 8.0), 600 mM
NaCl, 18% (NH4)2SO4. The column
was washed in 50 mM HEPES (pH 8.0) 600 mM NaCl,
9% (NH4)2SO4. The column was
developed with a reversed ammonium sulfate gradient; the protein
started to elute at 4% (NH4)2SO4.
The column fractions containing wild-type or mutant HSF fragments were
pooled and concentrated to a volume of less than 20 ml with a
Centriprep filtration unit (Millipore) at 10 kDa cut-off. The protein
solution was desalted on HiTrap columns (Amersham Pharmacia Biotech)
equilibrated in 50 mM Tris (pH 6.7). The desalted protein
was loaded onto a HiTrap heparin column (Amersham Pharmacia Biotech)
equilibrated in 50 mM Tris (pH 6.7). The column was
developed with a NaCl gradient and the protein eluted between 650 and
850 mM NaCl. The column fractions containing wild-type or
mutant HSF fragments were again pooled and concentrated to a volume of
less than 5 ml with a Centriprep 10 filtration unit (Millipore) at 10 kDa cut-off. If the protein appeared greater than 95% pure by
SDS-PAGE, then it was desalted on HiTrap columns (Amersham Pharmacia
Biotech) equilibrated in 50 mM Tris (pH 6.7). If the
protein appeared less than 95% pure by SDS-PAGE, then it was loaded
onto a HiLoad 16/60 Superdex 75 column (Amersham Pharmacia Biotech)
equilibrated in 50 mM Tris (pH 6.7). In either case, the
purified proteins were lyophilized to dryness and stored at
20 °C.
For subsequent analyses, the lyophilized protein was resuspended in the
appropriate buffer and protein concentration was determined by Lowry
protein assays or by absorbance at 280 nm using a protein extinction
coefficient of 32,290 cm
1
M
1.
DNA-binding Assays--
Binding of wild-type and mutant HSF
fragments to DNA was performed using variations of previously described
protocols (13, 31). Plasmid pBL3 (31), which contains an HSE with three
GAA repeats, was digested with XhoI and SpeI. The
145-base pair fragment was purified on a 4% Metaphor (BMA)-agarose gel
and the ends were labeled with T4 polynucleotide kinase and
[
-32P]ATP. Lyophilized protein was resuspended in a
small volume of 10 mM Tris (pH 8.0) and 0.1 mM
EDTA prior to diluting in the gel shift buffer. Binding of protein to
DNA was performed in 50 mM HEPES (pH 8.0), 50 mM NaCl, 10% glycerol, and 0.5 mg/ml bovine serum albumin.
-32P-Labeled 145-base pair fragment (0.75 fmol) was
mixed with a protein sample (1.8 fmol to 20 pmol) in a final volume of
20 µl and incubated at room temperature for 10 min. Reactions were
loaded onto polyacrylamide gels and electrophoresed as described
previously (31). Dried gels were used to expose Molecular Dynamics
PhosphorImager plates, and data were analyzed as described previously
(13).
Circular Dichroism Spectroscopy--
Lyophilized protein was
resuspended in 10 mM sodium phosphate, pH 7.0. CD spectra
were recorded on an Aviv CD spectrometer (model 62ADS). For scans,
measurements were taken at 25 °C at 2-nm intervals with a 1-s
averaging time and 1.5-nm bandwidth. For thermal melts, the wavelength
was held constant at 222 nm, while the temperature was raised at 2°
intervals from 4 to 94 °C with a 5-min equilibration time, 10-s
averaging time, and 1.5-nm bandwidth. The program NONLIN was used to
calculate the temperature at the inflection point of the unfolding
curve, which was assigned as the Tm value.
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RESULTS |
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Experimental Rationale-- In a previous study, we had used alanine-scanning mutagenesis, in combination with structural studies on the DNA-binding domain, to analyze systematically the surface residues of the HSF DNA-binding domain (25). The assay depended on the requirement of a functional HSF for yeast viability (3). We used the S. cerevisiae gene for the functional assay and mutated those residues predicted to be solvent accessible based on homology to the Kluyveromyces lactis structure (12). Not only are the sequences of the S. cerevisiae and K. lactis HSF DNA-binding domains highly homologous, but the proteins are functionally interchangeable (8).
Of the 64 mutants tested, we identified 6 that resulted in an inviable
phenotype, suggesting that those 6 residues were essential for HSF
function. One of these essential residues, Gly244, was
located at the tip of the "wing" (Fig.
2); mutation of this residue to alanine
caused the protein to be proteolyzed (data not shown). Another residue,
Trp194, lies in a hydrophobic pocket and is likely involved
in inter- or intramolecular contacts (25). Given the location of the
remaining four within or located near helix 3 (Fig. 2), the DNA
recognition helix, we postulated that those four residues were involved
in binding to DNA. This was later confirmed from analysis of a
co-crystal structure between the DNA-binding domain and a two-repeat
HSE in a tail-to-tail orientation (32). Of the remaining 58 residues that were not essential for yeast viability, 7 were defined as strictly
conserved and 12 were defined as highly conserved among all HSF
DNA-binding domains. In this study, we focused on these mutants that
were not essential for HSF function and looked specifically at their
level of transcriptional activity under constitutive and heat-induced
conditions.
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Transcriptional Activity of Surface Mutants--
To analyze the
transcriptional activity of the mutant HSFs, strains containing each of
the remaining 58 mutant HSFs were transformed with a plasmid containing
a
-galactosidase gene whose expression depends on a synthetic HSE
within a disabled CYC1 promoter. The transformed strains were assayed
for constitutive activity at 30 °C (Fig.
3A), as well as heat-inducible
activity after 30 min at 42 °C (Fig. 3B). Thirty-five of
the mutant HSFs were determined to be statistically different than
wild-type HSF at either the constitutive or induced levels (see
"Experimental Procedures" for details). Only six have decreased
constitutive activity, and three of those have increased induced
activity. The rest of the mutants have increased either constitutive or
induced levels of activity. Therefore, mutations in at least half of
the solvent-accessible residues of HSF can cause an increase in its
transcriptional activity. This strongly supports the idea that the
DNA-binding domain is involved in negative regulation of HSF's
transcriptional activity.
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The six mutants with decreased constitutive activity include
His220, a strictly conserved residue located at the turn
between helices 2 and 3; Val238, a highly conserved residue
located at the end of the third
-strand; and four nonconserved
residues located within the flexible wing (Fig. 2). Val238
and two of the residues in the wing also have increased induced activity.
The 29 residues with increased activity are located throughout the primary sequence of the protein. The mutants can be classified into three categories: those with increased constitutive and inducible activity (17), those with increased constitutive activity (1), and those with increased inducible activity (11). There does not appear to be a correlation with sequence conservation and activity classification, although mutations at all 7 strictly conserved surface residues and at 9 of the 12 highly conserved surface residues do cause at least some change in activity (Fig. 2).
Because of the availability of crystal structures of the K. lactis DNA-binding domain (12, 14), as well as the functional and
sequence homology between the K. lactis and S. cerevisiae HSF DNA-binding domains (8, 12, 25), we can map the
location of the mutants onto the structures (Fig.
4). The mutations with decreased
constitutive activity appear to map at or near the wing and away from
the DNA-binding surface (see cyan and blue
colors in Fig. 4, B and C). This
confirms a previous study that showed that deletion of the wing causes
a decrease in transcriptional activity (33). On the other hand, the
large subsets of mutations with either increased constitutive and heat
shock activity or with only increased heat shock activity are located
all over the structure (see purple and pink
colors in Fig. 4, B and C). This suggests that negative regulation via the DNA-binding domain is complex
and multifaceted.
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Focus on Six of the Strongest Mutants--
To study further the
relationship between the DNA-binding domain mutants and negative
regulation of transcriptional activity, we chose to focus on six of the
mutants with the largest increases in transcriptional activity. Four of
the mutations are at positions that are strictly conserved in all HSFs
(Lys178, Asn222, His236, and
Lys237), one is at a position that is highly conserved
(Asp185), and the sixth is at a position that is not
conserved (Arg206). The set of residues includes positively
charged, neutral, and negatively charged side chains, and they are
distributed throughout the domain (Fig.
5).
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To confirm that the mutations did not affect stability in vivo, we used Western blot analysis to compare the levels of protein for the wild-type and mutant HSFs. We used two different polyclonal antibodies against full-length HSF (gifts of P. Sorger and D. Gross) and probed lysates from both saturated and log-phase cultures. The alanine-substitutions did not appear to have any effect on steady-state levels of HSF in vivo (data not shown).
The Mutants Differentially Affect the N- and C-terminal Activation
Domains--
Although yeast HSF has two activation domains, yeast will
survive with HSF lacking either the N-terminal or C-terminal activation domain, i.e. with HSF-(66-833) or HSF-(1-583),
respectively. Because the domains have slightly different functions,
strains containing these different versions of HSF have different
constitutive and induced levels of transcriptional activity (7). In
order to analyze whether the mutations within the DNA-binding domain
were specific for a particular activation domain, we constructed
strains that contained truncated versions of wild-type and mutant HSFs, as well as the HSE-dependent lacZ fusion. Fig.
6 shows the constitutive and induced
level of transcriptional activity for the full-length and truncated
HSFs. The most striking result is that some of the mutations
differentially affect HSF activity dependent on the presence of a
specific activation domain.
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The mutants can be grouped into three classes: primary effect on the C-terminal activation domain, primary effect on the N-terminal activation domain, and mixed phenotype. For the mutation K237A, the increased activity is entirely due to the C-terminal activation domain. HSF-(1-583)K237A has similar constitutive and induced activity to HSF-(1-583) (Fig. 6C), whereas HSF-(66-833)K237A has dramatically increased constitutive and induced activity relative to HSF-(66-833) (Fig. 6B). For the mutations K178A, D185A, R206A, and H236A, the increased activity is almost entirely due to the N-terminal activation domain (Fig. 6, A and B, compare the level of activity for each mutant relative to wild-type). The mutation N222A has a mixed phenotype: HSF-(66-833)N222A retains a dramatic increase in the level of constitutive activity over wild-type HSF-(66-833) but not induced activity (Fig. 6B), whereas HSF-(1-583)N222A has the opposite (Fig. 6C).
The Mutant Phenotype Does Not Appear to Be Mediated via Changes in DNA-binding Affinity-- From the HSF-DNA co-crystal structure (32), we know that two of the residues make direct contact to the phosphate backbone (His236 and Lys237), whereas two of the residues make water-mediated contacts to the phosphate backbone (Lys178 and Asn222). Arg206 is involved in the dimer interface between two DNA-binding domains when bound to an HSE in the tail-to-tail orientation of NTTCNNGAAN, whereas Asp185 does not appear to be involved in any protein-protein or protein-DNA interfaces.
Because some of the mutations appear to be involved in DNA-binding contacts based on their location with respect to the co-crystal structure, it was important to analyze whether they affected DNA-binding affinity. Fragments of HSF containing the mutant DNA-binding domain and the wild-type trimerization domain were used in a gel-shift assay with a three-repeat HSE. We had previously shown that these fragments contained the same DNA-binding characteristics as full-length HSF (9).
None of the mutants were impaired or improved in their ability to form trimers or larger oligomeric species on DNA (data not shown). The mutants did have slightly increased apparent affinities for DNA, ranging from 1.1- to 3.8-fold over wild-type (Table I). It is possible that this increase in affinity could account for the increase in transcriptional activity seen for the mutant HSFs. However, there are several reasons to suggest that this is not the case. First, removal of an activation domain can cause some of the mutant HSF truncations to have similar levels of transcriptional activity as the same wild-type truncation (Fig. 6). Since the DNA-binding domains and DNA-binding sites were the same for all the truncations, it seems unlikely that DNA-binding affinity could account for the differences in activity for the full-length protein but not the truncations. Second, there is no correlation between the increase in DNA-binding affinity and the increase in transcriptional activity for the full-length HSFs; the mutant with the greatest increase in activity (K237A) has the lowest increase in affinity (1.1-fold over wild-type). Indeed, we had shown previously that this kind of small difference in the range of DNA-binding affinity does not correlate with differences in transcriptional activity (13, 14). Therefore, despite the contacts seen in the co-crystal structure, we conclude that the contacts to the DNA were not critical for the phenotype of these mutants.
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The Mutations Influence Structure and Thermal
Stability--
If the mutations within the DNA-binding domain are
affecting transcriptional activity by relieving negative regulation of the activation domains, it is possible that they do so by affecting the
structure of the DNA-binding domain. We used circular dichroism (CD)
spectroscopy to determine if the mutations influenced the secondary
structure characteristics of HSF. Fig. 7
shows the CD spectra for the wild-type HSF fragment in comparison to
the fragments containing each of the six strong mutations. Two of the
mutants, N222A and H236A, have CD spectra that are identical to
wild-type, suggesting that their secondary structures are not
perturbed. The other four mutants show some differences from wild-type;
K178A and K237A differ at the 208-nm minima, while D185A and R206A
differ at the 222-nm minima. It is possible that the structural changes found in these mutants indicate conformational changes in the DNA-binding domain variants that increase its ability to unmask the
activation domains in the absence of stress.
|
We also used CD spectroscopy to determine whether the thermal stability of the fragments was affected (Table II). One of the mutants, K237A, was not significantly changed from wild-type, whereas the other five had decreased thermal stabilities of 3 to 11 °C relative to the wild-type HSF fragment. It is possible that the destabilization of the DNA-binding domain in some of these mutants contributes to the increase in transcriptional activity via a thermally induced transition, as has been predicted for a series of mutations within the bulged second helix of the DNA-binding domain (13).
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DISCUSSION |
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We have studied the relationship between the DNA-binding domain and HSF's transcriptional activity under constitutive and induced conditions by analyzing a set of alanine-scanning mutants of the surface residues of the DNA-binding domain. More than half of these mutants affect transcriptional activity to some extent, with the majority of the mutations causing an increase in transcriptional activity under constitutive and/or induced conditions. The mutations are located throughout the DNA-binding domain and involve residues that cover approximately half of the domain's surface. Our results extend those from previous experiments suggesting that the DNA-binding domain is involved in the negative regulation of HSF's transcriptional activity (13-15, 22, 24).
Detailed studies on six of the strongest mutants have led to the following additional conclusions. First, the DNA-binding domain regulates the activity of both the N-terminal and C-terminal activation domains, and specific residues can be specific for a particular activation domain. This can be seen most clearly by comparing the results for K178A, whose phenotype is mediated almost entirely via the N-terminal activation domain and K237A, whose phenotype is mediated almost entirely via the C-terminal activation domain (Fig. 6). Second, the mutant phenotype, i.e. increased transcriptional activity, does not appear to be mediated via an increase in DNA-binding affinity (Table I). This is supported by the fact that the DNA-binding domain mutants have different phenotypes dependent on the number and type of activation domain present. Given that all of these transcriptional assays used the same synthetic HSE-dependent promoter, it seemed unlikely that the phenotype of the DNA-binding domain mutants would be due to changes in DNA-binding affinity.
At the same time, we find that some of the mutations affect the secondary structure of a fragment containing the DNA-binding and trimerization domains, whereas other mutations affect this fragment's thermal stability. There does not seem to be an exact correlation between those mutants whose structure is affected and those whose thermal stability is affected. K178A and K237A have the most dramatic effects on secondary structure, but K178A has a melting temperature that is 7° less than wild-type HSF, whereas K237A is as stable as wild-type. D185A and R206A, with moderate structural changes, have moderate decreases in thermal stability. N222A and H236A have identical secondary structure to wild-type HSF, but the most dramatic decrease in thermal stability.
In previous studies, we had discussed two potential models for how
mutations within the DNA-binding domain might affect transcriptional activity (13, 14). Removal of residues from the
-helical bulge in
the second helix of the DNA-binding domain significantly decreases the
thermal stability of the domain by at least 15 °C without appearing
to affect the overall structure. These mutants had an increase in
transcriptional activity of 4-6-fold. We suggested that the
DNA-binding domain might be sensing heat directly, with the decrease in
thermal stability causing the mutants to be structurally analogous to
the heat-induced state of HSF (13). Alternatively, we found that
substitution of the proline that is located at the center of the kink
in the same helix with a lysine, but not an alanine or aspartate,
caused a significant increase in transcriptional activity. The lysine
substitution did not affect the structure of the kink, but it did alter
the molecular surface of that face of the protein. We suggested that
this might affect the interaction of that surface of the DNA-binding
domain with either an ancillary factor or a regulatory region of HSF
(14).
Our current studies support those two models. N222A and H236A behave in a manner similar to the bulge-deletion mutants. They have decreased thermal stability of 10-11 °C with no apparent affect on structure, but they have an average of 4-fold increase in activity over wild-type HSF. K237A, on the other hand, has no decrease in thermal stability but a significant change in secondary structure and transcriptional activity. It is likely that this mutant is dramatically affecting the surface structure of the DNA-binding domain, perhaps causing a structural transition that mimics the heat-induced state.
It is also interesting to look at the thermal stability of the six mutants with respect to their influence on a specific activation domain. Three of the four mutants whose increase in constitutive activity depends on the N-terminal activation domain (K178A, D185A, and H236A) have the largest decrease in thermal stability (6 to 11 °C). This implies that the activity of the N-terminal activation domain is influenced by a thermally induced transition, which makes sense as it is more involved in the transient response to heat shock.
Our studies cannot differentiate between models of direct or indirect
interactions by the DNA-binding domains with the activation domains.
Using cross-linking studies, Bonner and colleagues (34) have shown that
the DNA-binding domain can interact directly with the N-terminal
activation domain, but not the C-terminal activation domain. This would
suggest that mutations such as K237A affect the ability of the
DNA-binding domain to interact with another protein that might function
to unmask the C-terminal activation domain.
| |
ACKNOWLEDGEMENTS |
|---|
We are indebted to Ramona Urbauer for help with cloning and to the DeGrado laboratory for the use of their CD spectrometer. We also thank Karen Flick, Eric Powers, Jeanne Hardy, Marco Cicero, Jamie Schlessman, and Scott Ferguson.
| |
FOOTNOTES |
|---|
* This work was supported by National Institutes of Health Grant GM44086.The costs of publication of this article were defrayed in part by the payment of page charges. The article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.
§ These authors contributed equally to this work and should be considered joint first authors.
To whom correspondence should be addressed: Dept. of
Biochemistry and Biophysics, University of Pennsylvania School of
Medicine, 813 Stellar-Chance, 422 Curie Blvd., Philadelphia, PA
19104-6089. Tel.: 215-573-7473; Fax: 215-573-2503; E-mail:
hnelson@mail.med.upenn.edu.
Published, JBC Papers in Press, August 16, 2001, DOI 10.1074/jbc.M106301200
2 E. E. Powers and H. C. M. Nelson, unpublished data.
| |
ABBREVIATIONS |
|---|
The abbreviations used are: HSF, heat shock transcription factor; HSE, heat shock element; PAGE, polyacrylamide gel electrophoresis.
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