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Acta Biochim Biophys Sin 2006, 38: 356-362

doi:10.1111/j.1745-7270.2006.00170.x

Effects of Heat Stress on Yeast Heat Shock Factor-Promoter Binding In Vivo

 

Ning LI1, Le-min ZHANG1*, Ke-Qin ZHANG1, Jing-shi DENG1, Ralf PR�NDL2&, and Fritz SCH�FFL2

 

1 Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming 650091, China;

2 Zentrum f�r Molekularbiologie der Pflanzen - Allgemeine Genetik, Eberhard-Karls-Universit�t T�bingen, 72076 T�bingen, Germany

 

Received: January 9, 2006

Accepted: March 22, 2006

This work was supported by the grants from the National Natural Science Foundation of China (No. 30560012), the Department of Science and Technology of Yunnan Province (2003C0012R, 2005NG05), the project sponsored by SRF for ROCS, SEM; and the grants from Deutsche Forschungsgemeinschaft (PR511/1-1; SFB446-A2)

& Present address: SerCon GmbH, Heinrich-von-Brentano-Sre. 2, D-55130 Mainz, Germany

*Corresponding author: Tel, 86-871-5031094; Fax, 86-871-5034838; E-mail, [email protected]

 

Abstract������� Heat shock factor-DNA interaction is critical for understanding the regulatory mechanisms of stress-induced gene expression in eukaryotes. In this study, we analyzed the in vivo binding of yeast heat shock factor (HSF) to the promoters of target genes ScSSA1, ScSSA4, HSP30 and HSP104, using chromatin immunoprecipitation. Previous work suggested that yeast HSF is constitutively bound to DNA at all temperatures. Expression of HSF target genes is regulated at the post-transcriptional level. However, our results indicated that HSF does not bind to the promoters of ScSSA4 and HSP30 at normal temperature (23 �C). Binding to these promoters is rapidly induced by heat stress at 39 �C. HSF binds to ScSSA1 and HSP104 promoters under non-stress conditions, but at a low level. Heat stress rapidly leads to a notable increase in the binding of HSF to these two genes. The kinetics of the level of HSF-promoter binding correlate well with the expression of target genes, suggesting that the expression of HSF target genes is at least partially the result of HSF-promoter binding stability and subsequent transcription stimulation.

 

Key words������� chromatin immunoprecipitation; heat shock factor; heat shock gene; yeast heat shock factor-promoter binding

 

Cells respond to elevated temperature and other physiological stresses by dramatically increasing the expression of heat shock proteins (HSPs), a set of proteins functioning as molecular chaperones, which are involved in the folding, trafficking, maturation and degradation of proteins. An increased accumulation of HSPs is essential for the survival of cells exposed to various stresses [1,2]. In eukaryotes, the expression of heat shock genes which encode HSPs is regulated by the binding of heat shock factors (HSFs) to heat shock gene promoter elements. heat shock element (HSE) is composed of tandem inverted repeats of a short consensus sequence 5'-nGAAn-3' [1]. The HSF-HSE interaction is conserved from yeast to human, but there is wide variability in the number of HSF genes in nature. Plants and mammals harbor multiple genes encoding HSF isoforms, with Arabidopsis thaliana possessing 21 distinct HSF genes and mammals possessing three genes [3,4]. The existence of multiple HSF isoforms might have a specialized function and regulate different target genes. Yeast, however, harbors only a single HSF which is thought to play multiple roles that are shared with the isoforms in higher eukaryotes [5,6]. Recent reports demonstrated yeast HSF is essential for heat-inducible transcription of not only HSPs but also genes encoding proteins involved in diverse cellular processes including growth, development, disease, aging, and in the complex metabolic reprogramming that occurs in response to stresses [7,8].

Considering the important role of HSF in the cellular homeostatic control, it is important to elucidate the regulatory mechanisms of HSF in cellular stress response. In plant, animal and mammalian cells, HSF is present in a latent, monomeric state under normal conditions; the HSF DNA-binding activity depends on the trimerization of monomeric HSF subunits upon heat stress, and the event of binding triggers the transcriptional activation of target genes [4,9,10]. In yeast, early studies using in vitro binding assay and genetic methods suggested that the stress inducing expression of HSF target genes is regulated at the post-transcriptional level, for instance, the heat-inducible phosphorylation of the HSE-bound HSF was suggested to be responsible for the activation of heat shock gene expression, whereas HSF binding to HSEs is strictly constitutive [5,11,12]. However, in vivo, protein-DNA binding is determined by additional factors which stimulate or inhibit binding. Later, in vivo footprinting was used to study protein-DNA interaction on the yeast HSP82 gene, and it was proposed that HSF binds to strong HSEs (three consensuses) constitutively, but binding to weak HSEs (poor matches to consensus) is dependent on heat stress [13,14]. However, footprinting does not identify the interacting protein.

In this report, we analyzed the in vivo binding of HSF to target genes using cross-linking chromatin immunoprecipitation (X-ChIP) which is thought to allow both the identification of the protein and the interacting DNA sequence [15]. Our results showed that HSF binds to different targets in a different manner. HSF binding to ScSSA4 and HSP30 is heat stress dependent. HSF binds to ScSSA1 and HSP104 under non-stress conditions, but at a low level; heat stress apparently increases the binding level. The kinetics of binding correlate well with target gene expression, suggesting that the binding plays a role in the transcriptional stimulation of target genes

 

 

Materials and methods

 

Construction of expression vectors

 

Plasmid pQE30 was isolated from Escherichia coli TG1 (Qiagen, Carlsbad, USA) using a Nucleospin Multi-8 plasmid kit (Machery-Nagel, D�ren, Germany). The yeast HSF entire coding region DNA fragment (yHSF) was inserted, containing an adaptor of the PstI restriction site located after the translation stop codon, and an adaptor of the SacI restriction site located before the translation start codon. They were produced by polymerase chain reaction (PCR) using primer pair QE30-hsf/u (5'-GCACTGCAGCTATTTCTTAACTCGTTTGG-3') and QE30-hsf/d (5'-GCAGAGCTCATGAATAATGCTGCAAATACA-3') at annealing temperature 53 �C.

Plasmid pQE30 and the PCR product of yHSF were digested with SacI, followed by PstI. After ligation by T4 DNA ligase, the ligated construct pQE30/His-yHSF was transformed to TG1 by electroporation. Positive colonies were identified by hybridization with the HSF gene (coding sequence) probe which was synthesized using the PCR product of yHSF as template. The constructs were verified by sequencing. The colony with the verified construct was chosen for expressing the recombinant peptides.

 

Preparation of affinity-purified antibodies

 

Yeast His6-HSF was expressed from TG1(pQE30/yHSF) and purified using denaturing-renaturing purification according to the QIAexpressionist (Qiagen), verified by Western blot analysis and used for the generation of antiserum against yeast HSF in rabbit. For the generation of monospecific antibodies, His6-HSF peptide was coupled to AminoLink Plus Coupling Gel (Pierce, Rockford, USA) and the affinity purification of the antibodies was carried out using ImmunoPure IgG Elution Buffer (Pierce).

 

Chromatin immunoprecipitation

 

Yeast cells (Saccharomyces cerevisiae, strain Y190) were grown in 50 ml SD-Leu medium (26.7 g/L minimal synthetic defined base, 0.69 g/L Leu drop out supplement, ph 5.8) (BD Biosciences Clontech, Palo Alto, USA) to an optical density (OD600) of 2 at 23 �C, then heated at 39 �C for 0, 10, 30, and 60 min. Cell cultures were cross-linked with 1% formaldehyde and chromatin was isolated according to the method described by Strahl-Bolsinger et al. [16]. Four hundred microliters of the resulting chromatin from each sample was sonicated for 1020 s (resulting in fragment sizes 0.3-0.5 kb) using a Branson Digital Sonifier (S-250D; Branson Ultrasonic, Danbury, USA) at 40% output (keeping the sample on ice during sonication). The chromatin extracts were centrifuged at 10,000 rpm at 4 �C for 20 min, and the supernatants were filtered through a 0.22 mm filter.

Ten micrograms of affinity-purified anti-HSF antibodies was added to 400 ml chromatin extract samples and incubated at 4 �C for 3 h, then 60 ml protein A-agarose preincubated with 1% BSA was added to block non-specific binding, and the samples were incubated at 4 �C for 30 min. Subsequently, the resin was washed and the immunoprecipitated material was eluted according to the method described by Strahl-Bolsinger et al. [16]. Eighty microliters of the resulting elution material was digested by adding 80 ml of proteinase K (1 mg/ml) in proteinase K buffer (50 mM Tris, 10 mM EDTA and 0.3% sodium dodecylsulfate), incubated at 60 �C for 16 h (from this point, 80 ml chromatin extract was processed in parallel to obtain total genomic DNA), extracted twice with phenol/CHCl3, and once with CHCl3. DNAs were precipitated by ethanol and dissolved in 20 ml TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8.0).

 

PCR analysis of immunoprecipitated DNA

 

Immunoprecipitated DNA was analyzed by PCR. One microlitre of immunoprecipitated material was added to 20 ml PCR reaction mixture (50 mM KCl, 20 mM Tris-HCl, pH 8.3, 0.05% Tween-20, 0.01 mg/ml gelatin, 2.5 mM MgCl2, 2.5 mM each dNTP, 1 U Taq polymerase). PCR reaction was carried out for 30 cycles (unless elsewhere indicated) of 20 s at 94 �C, 20 s at 49-56 �C and 10 s at 72 �C. The PCR products were separated on a 10% polyacrylamide gel and visualized by staining with ethidium bromide. The following primer pairs were used to detect target genes: ScSSA1-307u, 5'-TCAACTAAAATCTGGAGAAAA-3'; ScSSA1-314d, 5'-CGGAACGTTTAGAAGCTGTCATT-3', 53 �C; ScSSA1+1893d, 5'-GGTGCTCCTCCAGCTCCA-3'; ScSSA1+1899u, 5'-TCAACGGTTGGACCTTCA-3', 54 �C; ScSSA1+1193d, 5'-TGTCGCTCCATTATCCTT-3'; ScSSA1+1199u, 5'-CACCACCAGCAGTTTCAA-3', 54 �C; ScSSA4-301u, 5'-AACTCACCGGGCAAAAGA-3'; ScSSA4-308d, 5'-AATGTAATAGGTTTCAAAG-3', 49 �C; ScSSA4-364u, 5'-GAGAGTACATACCGGAATG-3'; ScSSA4-429d, 5'-ACTAAATTACGTTCATAGGG-3', 54 �C; ScSSA4+1807d, 5'-GTTAGATGCTTCGCAAGC-3'; ScSSA4+1814u, 5'-TCCTTGTATTCCTCGGTG-3', 54 �C; HSP30-503u, 5'-AAGCACGCTTTCGATGCG-3'; HSP30-514d, 5'-CGTAGGAGGATTCTCTCA-3', 52 �C; HSP104-131u, 5'-TGAGGCAAGATTACAATGC-3'; HSP104-143d, 5'-CTTATGCAACCTGCCAGA-3', 52 �C; YPL231W-1170u, 5'-AGTGACTTGCTTGCTCCTC-3'; YPL231W-1206d, 5'-GATTCTTTGCATAAGAGGCTA-3', 55�C. Primers were named according to the gene and the distance of the 3' nucleotide relative to the ATG translation start codon. The annealing temperatures are given.

 

 

Results

 

HSF binding site detected at high resolution by cross-linking chromatin immunoprecipitation and PCR analysis

 

To detect HSF binding to target in vivo, we employed the X-ChIP technique and PCR analysis for immunoprecipitated DNA. We successfully detected the binding of yeast HSF to the ScSSA4 gene in vivo and examined the binding site at high resolution. Yeast cells were heat stressed at 39 �C for 10 min, followed by formaldehyde cross-linking and immunoprecipitation using affinity-purified yeast HSF antibodies. The immunoprecipitated DNAs were analyzed by PCR using different primer pairs. The genes and distribution of primers are shown in Fig. 1. For positive controls, total genomic DNAs were used as the templates for PCR amplification. For negative controls, we used immunoprecipitates without prior formaldehyde cross-linking or without HSF antibodies. The results are shown in Fig. 2. Two primer pairs, ScSSA4-364u/-429d and ScSSA4-301u/-308d, were used, which were located in the promoter region of ScSSA4. The space between primers in ScSSA4-364u/-429d and ScSSA4-301u/-308d was 64 and 6 nucleotides, respectively. Both primer pairs properly produced specific PCR products and gave similar results. Heat stressed samples gave strong signals after 40 cycles of amplification, but there were weak background signals for negative controls and weak signals for the sample without heat stress. However, the signals of the heat stressed samples were significantly stronger than those of other samples, indicating heat stress induced HSF binding to the ScSSA4 gene. The weak bands of the sample without heat stress were comparable with the bands for the negative controls. With the PCR cycle reduced to 30 cycles, the heat stressed samples still gave clear signals, whereas the signals were abolished for both the negative controls and the sample without heat stress, indicating HSF did not bind to ScSSA4 promoter under non-stress conditions, but the binding occurred after heat stress.

To determine the spatial specificity of HSF binding, we amplified immunoprecipitates using primer pair YPL231W-1206d/-1170u located in a randomly chosen YPL231W promoter. The results showed that no signal was detected and HSF did not bind to the non-target promoter. To further define the binding site, we analyzed whether HSF binds to the space adjacent to the ScSSA4 promoter by using primer pair ScSSA4+1807d/+1814u located in the coding region of the ScSSA4 gene, approximately 1800 bp away from the start codon. No PCR signal was detected with this primer pair, demonstrating the X-ChIP technique could detect the HSF binding site at high resolution.

 

Effects of heat stress on binding of HSF to target genes in vivo

 

Early experiments suggested that yeast HSF was localized in the nucleus and bound to the target gene promoter, even in the absence of heat stress. However, the above results showed that HSF binding to the ScSSA4 promoter is dependent on heat stress. This contradiction prompted us to further investigate the effects of heat stress on HSF binding to different target promoters.

Based on multiple independent chromatin immunoprecipitation experiments, we analyzed the dynamic association of HSF with the promoters of ScSSA1, ScSSA4, HSP30, and HSP104 genes in vivo. Yeast cells were heat shocked at 39 �C for 0, 10, 30 and 60 min, followed by formaldehyde cross-linking and immunoprecipitation. The PCR amplification of immunoprecipitated DNA using primer pairs located in different promoter regions are shown in Fig. 3. The results showed that HSF bound to ScSSA1 and HSP104 promoters under non-stress conditions, whereas no binding occurred to ScSSA4 and HSP30 without heat stress. Heat stress rapidly increased HSF binding to ScSSA1 and HSP104 promoters and induced HSF binding to ScSSA4 and HSP30 promoters. The level of HSF binding to these four promoters reached a peak after 10 min of heat stress and declined with continuous exposure to heat stress for up to 1 h, however, it was slightly higher than basal level in the cases of ScSSA1 and HSP104. The negative controls without formaldehyde cross-linking or without antibodies did not give PCR signals. Therefore we excluded the effect of the background signal. Two primer pairs located in the ScSSA1 coding regions and one primer pair situated in the YPL231W promoter region did not have PCR signals, indicating HSF did not bind to non-target DNA. These results suggested that HSF binds to different targets in a different manner, constitutively or heat stress-dependently, and heat stress apparently increases binding affinity.

The comparison of HSF binding levels in the time-course experiment with the profiling of target gene expression within published data indicates that HSF binding correlates well with target gene expression, suggesting that induced or increased HSF binding plays an important role in the regulation of yeast target gene activation.

 

 

Discussion

 

It was initially thought that yeast HSF trimers constitutively bind to HSEs under both normal and heat stress conditions. Later, based on in vivo footprinting experiments, Erkine et al. [13] and Giardina and Lis [14] proposed that HSF binding to strong HSEs of HSP82 is constitutive, but binding to weak HSEs is induced by heat stress. However, our results indicate that heat stress significantly affects binding behavior, and that HSF binds to different promoters in a different manner. Binding to HSP30 and ScSSA4 genes is heat stress-dependent. HSF does not bind to these two genes under non-stress conditions, even the ScSSA4 promoter that contains strong HSE. HSF binds to ScSSA1 and HSP104 promoters under non-stress conditions, but at a low level. Heat stress rapidly leads to a notable increase in the binding of HSF to these two genes. Interestingly, the HSF binding level is attenuated by prolonged exposure to heat stress. A similar phenomenon was previously found in higher eukaryotes and it was proposed that the binding stability is negatively regulated by the association of HSF with other proteins, including HSP70 and HSP90 [17,18].

However, our experiments suggested that HSE is not the sole determinant of HSF binding. For instance, previously published work proposed that HSP30 is not under the control of HSF because of the lack of a typical HSE in the HSP30 promoter [19]. Our results showed that HSF binds to HSP30 in a heat-induced manner. We also verified the lack of HSF binding to the YPL231W promoter, which contains a consensus HSE. Although HSE is known to be important for HSF binding, the lack of HSF binding to the YPL231W promoter and the heat-induced binding to HSP30 suggest that its presence is clearly not the sole determinant of whether a promoter is bound and activated by HSF. It appears that HSF binding behavior in yeast is more complex than previously thought.

In order to analyze the putative effects of heat stress-induced or increased HSF binding on transcriptional activities of target genes, we examined the gene expression in S. cerevisiae within published data. The ScSSA4 mRNA level rapidly increased after 15 min and 30 min of heat stress at 39 �C and declined after 60 min of heat stress [11]. HSP30 mRNA was not detectable under normal conditions; however, the expression was induced by heat stress and other stresses [19]. The work by Causton et al. [20] showed that the expression level of ScSSA4, HSP104 and ScSSA1 was increased by 95-, 7- and 3-fold over basal levels, respectively, after 15 min of heat stress, and subsequently declined during continuous heat stress [20]. The timing of induction and the decline of the mRNA correlate well with HSF binding to the target genes in our time-course experiment, suggesting that expression of the HSF target genes is, at least in part, the result of the HSF-promoter binding stability and the consequent transcription stimulation, similar to that of higher eukaryotes [10]. This information, along with the findings on the role of heat-inducible phosphorylation of HSF in the expression of target genes, would promote our understanding of the complexity of yeast HSF regulatory mechanisms.

In our experiments, the X-ChIP technique was excellent for detecting HSF target DNA. However, it must be noted that immunoprecipitated DNA is relative enrichment of targets. To exclude background signals, it is essential to use negative controls in each experiment and design the appropriate number of PCR cycles. Only the signals produced by immuno-enriched targets, shown to be significantly stronger than the background signals produced by negative controls, can be considered. Furthermore, by carefully reducing the number of cycles, background signals were abolished, whereas the signals of the heat shock samples still existed. Therefore we could clearly determine the true binding signal. Our experiments also demonstrated that PCR analysis of target DNA is accurate in detecting binding sites. Only the primer pair located in the promoter region gave signals, whereas the primer pair located in the adjacent coding region of the same gene did not. To investigate the binding site and non-binding site at high resolution, we designed primers that were closely spaced in each primer pair and resulted in a PCR product with a short fragment (41-175 bp). Because the PCR reactions were carried out in a short phase of synthesis (10 s at 72 �C), the primer pairs listed in this report produced proper PCR products, and the specificity of the PCR products was further verified by sequencing in the analysis of a randomly chosen sample. However, we also found that some primer pairs did not work well in the amplification of such a short fragment, so it is necessary to test multiple primer pairs and choose the most suitable. However, with the digestion of formaldehyde-fixed chromatin with nonspecific proteinases, such as proteinase K, it is difficult to yield a completely peptide-free DNA [21]. Other cross-linking agents, such as ultraviolet light, also cause significant DNA damage [22]. These DNA modifications hamper the PCR analysis as PCR techniques require the DNA integrity for primer extension. The short space between primers would minimize the effect of DNA damage on PCR.

 

 

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