NORMAL GENOMIC

• Cicero MP, Hubl ST, Harrison CJ, Littlefield O, Hardy JA, Nelson HC
• The wing in yeast heat shock transcription factor (HSF) DNA-binding domain is required for full activity.
• Nucleic Acids Res. 2001; 29: 1715-23
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• The yeast heat shock transcription factor (HSF) belongs to the winged helix family of proteins. HSF binds DNA as a trimer, and additional trimers can bind DNA co-operatively. Unlike other winged helix-turn-helix proteins, HSF's wing does not appear to contact DNA, as based on a previously solved crystal structure. Instead, the structure implies that the wing is involved in protein-protein interactions, possibly within a trimer or between adjacent trimers. To understand the function of the wing in the HSF DNA-binding domain, a Saccharomyces cerevisiae strain was created that expresses a wingless HSF protein. This strain grows normally at 30 degrees C, but shows a decrease in reporter gene expression during constitutive and heat-shocked conditions. Removal of the wing does not affect the stability or trimeric nature of a protein fragment containing the DNA-binding and trimerization domains. Removal of the wing does result in a decrease in DNA-binding affinity. This defect was mainly observed in the ability to form the first trimer-bound complex, as the formation of larger complexes is unaffected by the deletion. Our results suggest that the wing is not involved in the highly co-operative nature of HSF binding, but may be important in stabilizing the first trimer bound to DNA.

• Ahn SG, Liu PC, Klyachko K, Morimoto RI, Thiele DJ
• The loop domain of heat shock transcription factor 1 dictates DNA-binding specificity and responses to heat stress.
• Genes Dev. 2001; 15: 2134-45
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• Eukaryotic heat shock transcription factors (HSF) regulate an evolutionarily conserved stress-response pathway essential for survival against a variety of environmental and developmental stresses. Although the highly similar HSF family members have distinct roles in responding to stress and activating target gene expression, the mechanisms that govern these roles are unknown. Here we identify a loop within the HSF1 DNA-binding domain that dictates HSF isoform specific DNA binding in vitro and preferential target gene activation by HSF family members in both a yeast transcription assay and in mammalian cells. These characteristics of the HSF1 loop region are transposable to HSF2 and sufficient to confer DNA-binding specificity, heat shock inducible HSP gene expression and protection from heat-induced apoptosis in vivo. In addition, the loop suppresses formation of the HSF1 trimer under basal conditions and is required for heat-inducible trimerization in a purified system in vitro, suggesting that this domain is a critical part of the HSF1 heat-stress-sensing mechanism. We propose that this domain defines a signature for HSF1 that constitutes an important determinant for how cells utilize a family of transcription factors to respond to distinct stresses.

• Goodson ML, Hong Y, Rogers R, Matunis MJ, Park-Sarge OK, Sarge KD
• Sumo-1 modification regulates the DNA binding activity of heat shock transcription factor 2, a promyelocytic leukemia nuclear body associated transcription factor.
• J Biol Chem. 2001; 276: 18513-8
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• Heat shock transcription factor 2 (HSF2) is a transcription factor that regulates heat shock protein gene expression, but the mechanisms regulating the function of this factor are unclear. Here we report that HSF2 is a substrate for modification by the ubiquitin-related protein SUMO-1 and that HSF2 colocalizes in cells with SUMO-1 in nuclear granules. Staining with anti-promyelocytic leukemia antibodies indicates that these HSF2-containing nuclear granules are PML bodies. Our results identify lysine 82 as the major site of SUMO-1 modification in HSF2, which is located in a "wing" within the DNA-binding domain of this protein. Interestingly, SUMO-1 modification of HSF2 results in conversion of this factor to the active DNA binding form. This is the first demonstration that SUMO-1 modification can directly alter the DNA binding ability of a transcription factor and reveals a new mechanism by which SUMO-1 modification can regulate protein function.

• Lee S et al.
• The yeast heat shock transcription factor changes conformation in response to superoxide and temperature.
• Mol Biol Cell. 2000; 11: 1753-64
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• In vitro DNA-binding assays demonstrate that the heat shock transcription factor (HSF) from the yeast Saccharomyces cerevisiae can adopt an altered conformation when stressed. This conformation, reflected in a change in electrophoretic mobility, requires that two HSF trimers be bound to DNA. Single trimers do not show this change, which appears to represent an alteration in the cooperative interactions between trimers. HSF isolated from stressed cells displays a higher propensity to adopt this altered conformation. Purified HSF can be stimulated in vitro to undergo the conformational change by elevating the temperature or by exposing HSF to superoxide anion. Mutational analysis maps a region critical for this conformational change to the flexible loop between the minimal DNA-binding domain and the flexible linker that joins the DNA-binding domain to the trimerization domain. The significance of these findings is discussed in the context of the induction of the heat shock response by ischemic stroke, hypoxia, and recovery from anoxia, all known to stimulate the production of superoxide.

• Mathew A, Shi Y, Jolly C, Morimoto RI
• Analysis of the mammalian heat-shock response. Inducible gene expression and heat-shock factor activity.
• Methods Mol Biol. 2000; 99: 217-55

• Liu PC, Thiele DJ
• Modulation of human heat shock factor trimerization by the linker domain.
• J Biol Chem. 1999; 274: 17219-25
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• Heat shock transcription factors (HSFs) are stress-responsive proteins that activate the expression of heat shock genes and are highly conserved from bakers' yeast to humans. Under basal conditions, the human HSF1 protein is maintained as an inactive monomer through intramolecular interactions between two coiled-coil domains and interactions with heat shock proteins; upon environmental, pharmacological, or physiological stress, HSF1 is converted to a homotrimer that binds to its cognate DNA binding site with high affinity. To dissect regions of HSF1 that make important contributions to the stability of the monomer under unstressed conditions, we have used functional complementation in bakers' yeast as a facile assay system. Whereas wild-type human HSF1 is restrained as an inactive monomer in yeast that is unable to substitute for the essential yeast HSF protein, mutations in the linker region between the DNA binding domain and the first coiled-coil allow HSF1 to homotrimerize and rescue the viability defect of a hsfDelta strain. Fine mapping by functional analysis of HSF1-HSF2 chimeras and point mutagenesis revealed that a small region in the amino-terminal portion of the HSF1 linker is required for maintenance of HSF1 in the monomeric state in both yeast and in transfected human 293 cells. Although linker regions in transcription factors are known to modulate DNA binding specificity, our studies suggest that the human HSF1 linker plays no role in determining HSF1 binding preferences in vivo but is a critical determinant in regulating the HSF1 monomer-trimer equilibrium.

• Nakai A
• New aspects in the vertebrate heat shock factor system: Hsf3 and Hsf4.
• Cell Stress Chaperones. 1999; 4: 86-93

• Soncin F, Prevelige R, Calderwood SK
• Expression and purification of human heat-shock transcription factor 1.
• Protein Expr Purif. 1997; 9: 27-32
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• Heat-shock factor 1 (HSF1) is a 57-kDa cytoplasmic protein which binds to the promoters of heat-shock genes and activates transcription during heat shock. We describe here the expression and purification of the 529 amino acids form of human HSF1. We designed a new and complete purification protocol involving ammonium sulfate precipitation, heparin-Sepharose affinity, and ion-exchange chromatography, which allows the purification of large amounts of pure and active recombinant protein. HSF1 isolated by this method is pure as that assessed by SDS-PAGE and reverse-phase HPLC. The purified protein is recognized by specific anti-HSF1 antibodies, binds to heat-shock elements, and activates the promoter of the heat-shock protein 70A gene in vitro.

• Torres FA, Bonner JJ
• Genetic identification of the site of DNA contact in the yeast heat shock transcription factor.
• Mol Cell Biol. 1995; 15: 5063-70
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• The heat shock transcription factor (HSF), a trimeric transcription factor, activates the expression of heat shock genes in eukaryotes. We have isolated mutations in the HSF1 gene from Saccharomyces cerevisiae that severely compromise the ability of HSF to bind to its normal binding site, repeats of the module nGAAn. One of these mutations, Q229R, shows a "new specificity" phenotype, in which the protein prefers the mutant sequence nGACn. These results identify the region of HSF that contacts DNA, in complete agreement with the crystal structure of HSF of Kluyveromyces lactis and the nuclear magnetic resonance data from HSF of Drosophila melanogaster. To determine the orientation of the DNA-binding domain on the nGAAn motif, we performed site-specific cross-linking between cysteine residues of single-cysteine substitutions. Cysteines placed at the N terminus of the DNA contact helix formed cross-links readily, while cysteines placed at the C terminus of the helix did not.

• Hubl ST, Owens JC, Nelson HC
• Mutational analysis of the DNA-binding domain of yeast heat shock transcription factor.
• Nat Struct Biol. 1994; 1: 615-20
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• Both randomized oligonucleotide cassette mutagenesis and site-directed mutagenesis have been used in combination with a yeast genetic screen to identify critical residues in the DNA-binding domain of heat shock transcription factor from Saccharomyces cerevisiae. Most of the surface residues in this highly conserved domain can be changed to alanine with no observable effect on function. Of nine critical residues identified in this screen, five are within helix alpha 3, previously designated as the probable DNA recognition helix in the crystal structure of the Kluyveromyces lactis protein. The other four residues may be involved in DNA-binding or protein-protein interactions.

• Flick KE, Gonzalez L Jr, Harrison CJ, Nelson HC
• Yeast heat shock transcription factor contains a flexible linker between the DNA-binding and trimerization domains. Implications for DNA binding by trimeric proteins.
• J Biol Chem. 1994; 269: 12475-81
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• All heat shock transcription factors (HSFs) share two regions of homology, identified as the DNA binding and trimerization regions. The DNA binding region consists of two parts, an 89-amino-acid minimal DNA-binding domain and an additional 21 amino acids which are not necessary for specific DNA binding of a monomeric DNA-binding domain. These 21 amino acids may act as a flexible linker between the DNA-binding and trimerization domains. Saccharomyces cerevisiae HSF has an additional 52 amino acids between the proposed flexible linker and the trimerization domain. Deletion of this unique region has no effect on the structural integrity or essential in vivo functions of HSF. To investigate the role of the 21-amino-acid proposed linker, a series of internal deletions was created in fragments containing the DNA-binding and trimerization domains. The deletions have no effect on the structural integrity of the protein as assayed by circular dichroism spectroscopy. However, alterations of the linker do affect affinity of trimeric HSF binding to its target DNA. In addition, deletion of part or all of the proposed linker from full-length yeast HSF, an essential protein, disrupts growth of yeast.

• Morimoto RI
• Cells in stress: transcriptional activation of heat shock genes.
• Science. 1993; 259: 1409-10

• Peteranderl R, Nelson HC
• Trimerization of the heat shock transcription factor by a triple-stranded alpha-helical coiled-coil.
• Biochemistry. 1992; 31: 12272-6
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• We have isolated and characterized a 91 amino acid fragment of the heat shock transcription factor from both Saccharomyces cerevisiae and Kluyveromyces lactis. The two protein fragments behave similarly: they form homotrimers, as indicated by sedimentation equilibrium and cross-linking, and contain approximately 80% alpha-helix, as indicated by circular dichroism. Sedimentation velocity and diffusion coefficients indicate that they have an elongated, nonspherical shape. We conclude the following: these fragments contain a domain which forms a trimer via a triple-stranded alpha-helical coiled-coil, similar to that found in influenza hemagglutinin.