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Mutational analysis of the DNA-binding domain of yeast heat shock transcription factor

Abstract

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 α3, 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.

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References

  1. Lis, J. & Wu, C. Protein traffic on the heat shock promoter: parking, stalling, and trucking along. Cell 74, 1–4 (1993).

    Article  CAS  Google Scholar 

  2. Wiederrecht, G., Seto, D. & Parker, C.S. Isolation of the gene encoding the S. cerevisiae heat shock transcription factor. Cell 54, 841–853 (1988).

    Article  CAS  Google Scholar 

  3. Flick, K.E., Gonzalez, L., Harrison, C.J. & Nelson, H.C.M. Yeast heat shock transcription factor contains a flexible linker between the DNA-binding and trimerization domains. J. biol. Chem. 269, 12475–12481 (1994).

    CAS  PubMed  Google Scholar 

  4. Sorger, P.K. & Nelson, H.C. Trimerization of a yeast transcriptional activator via a coiled-coil motif. Cell 59, 807–813 (1989).

    Article  CAS  Google Scholar 

  5. Harrison, C.J., Bohm, A.A. & Nelson, H.C.M. Crystal structure of the DNA binding domain of the heat shock transcription factor. Science 263, 224–227 (1994).

    Article  CAS  Google Scholar 

  6. Schultz, S.C., Shields, G.C. & Steitz, T.A. Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees. Science 253, 1001–1007 (1991).

    Article  CAS  Google Scholar 

  7. Vuister, G.W., Kim, S.J., Wu, C. & Bax, A. NMR evidence for similarities between the DNA-binding regions of Drosophila melanogaster heat shock factor and the helix-turn-helix and HNF-3/ forkhead families of transcription factors. Biochemistry 33, 10–6 (1994).

    Article  CAS  Google Scholar 

  8. Xiao, H. & Lis, J.T. Germline transformation used to define key features of heat-shock response elements. Science 239, 1139–1142 (1988).

    Article  CAS  Google Scholar 

  9. Amin, J., Ananthan, J. & Voellmy, R. Key features of heat shock regulatory elements. Molec. Cell. Biol. 8, 3761–3769 (1988).

    Article  CAS  Google Scholar 

  10. Perisic, O., Xiao, H. & Lis, J.T. Stable binding of Drosophila heat shock factor to head-to-head and tail-to-tail repeats of a conserved 5 bp recognition unit. Cell 59, 797–806 (1989).

    Article  CAS  Google Scholar 

  11. Kim, S.-J., Tsukiyama, T., Lewis, M.S. & Wu, C. Interaction of DNA-bindig domain of Drosophila heat shock factor with its cognate DNA site: A thermodynamic analysis using analytical ultracentrifugation. Prot. Sci. 3, (1994).

  12. Amin, J., Fernandez, M., Ananthan, J., Lis, J.T. & Voellmy, R. Cooperative binding of heat shock transcription factor to the Hsp70 promoter in vivo and in vitro. J. biol. Chem. 269, 4804–4811 (1994).

    CAS  PubMed  Google Scholar 

  13. Gross, D.S., English, K.E., Collins, K.W. & Lee, S.W. Genomic footprinting of the yeast HSP82 promoter reveals marked distortion of the DNA helix and constitutive occupancy of heat shock and TATA elements. J. molec. Biol. 216, 611–631 (1990).

    Article  CAS  Google Scholar 

  14. Rye, H.S., Drees, B.L., Nelson, H.C. & Glazer, A.N. Stable fluorescent dye-DNA complexes in high sensitivity detection of protein-DNA interaction. Application to heat shock transcription factor. J. biol. Chem. 268, 25229–25238 (1993).

    CAS  PubMed  Google Scholar 

  15. Liu-Johnson, H.N., Gartenberg, M.R. & Crothers, D.M. The DNA binding domain and bending angle of E. coli CAP protein. Cell 47, 995–1005 (1986).

    Article  CAS  Google Scholar 

  16. Bonner, J.J., Heyward, S. & Fackenthal, D.L. Temperature-dependent regulation of a heterologous transcriptional activation domain fused to yeast heat shock transcription factor. Molec. Cell Biol. 12, 1021–1030 (1992).

    Article  CAS  Google Scholar 

  17. Silar, P., Butler, G. & Thiele, D.J. Heat shock transcription factor activates transcription of the yeast metallothionein gene. Molec. Cell Biol. 11, 1232–1238 (1991).

    Article  CAS  Google Scholar 

  18. Yang, W.M., Gahl, W. & Hamer, D. Role of heat shock transcription factor in yeast metallothionein gene expression. Molec. Cell Biol. 11, 3676–3681 (1991).

    Article  CAS  Google Scholar 

  19. Sorger, P.K. & Pelham, H.R. Yeast heat shock factor is an essential DNA-binding protein that exhibits temperature-dependent phosphorylation. Cell 54, 855–864 (1988).

    Article  CAS  Google Scholar 

  20. Jakobsen, B.K. & Pelham, H.R. A conserved heptapeptide restrains the activity of the yeast heat shock transcription factor. EMBO J. 10, 369–375 (1991).

    Article  CAS  Google Scholar 

  21. Jakobsen, B.K. & Pelham, H.R. Constitutive binding of yeast heat shock factor to DNA in vivo. Molec. Cell Biol. 8, 5040–5042 (1988).

    Article  CAS  Google Scholar 

  22. Kunkel, T.A. Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc. natn Acad. Sci. U.S.A. 82, 488–492 (1985).

    Article  CAS  Google Scholar 

  23. Hill, D.E., Oliphant, A.R. & Struhl, K. Mutagenesis with degenerate oligonucleotides: an efficient method for saturating a defined DNA region with base pair substitutions. Meth. Enzymol. 155, 558–568 (1987).

    Article  CAS  Google Scholar 

  24. Reidhaar-Olson, J.F. & Sauer, R.T. Combinatorial cassette mutagenesis as a probe of the informational content of protein sequences. Science 241, 53–57 (1988).

    Article  CAS  Google Scholar 

  25. Bowie, J.U., Reidhaar, O.J., Lim, W.A. & Sauer, R.T. Deciphering the message in protein sequences: tolerance to amino acid substitutions. Science 247, 1306–1310 (1990).

    Article  CAS  Google Scholar 

  26. Cunningham, B.C. & Wells, J.A. High-resolution epitope mapping of hGH-receptor interactions by alanine-scanning mutagenesis. Science 244, 1081–1085 (1989).

    Article  CAS  Google Scholar 

  27. Wells, J.A. Systematic mutational analyses of protein-protein interfaces. Meth. Enzymol. 202, 390–411 (1991).

    Article  CAS  Google Scholar 

  28. Pabo, C.O. & Sauer, R.T. Transcription factors: structural families and principles of DNA recognition. A. Rev. Biochem. 61, 1053–1095 (1992).

    Article  CAS  Google Scholar 

  29. Shore, D. & Nasmyth, K. Purification and cloning of a DNA binding protein from yeast that binds to both silencer and activator elements. Cell 51, 721–732 (1987).

    Article  CAS  Google Scholar 

  30. Elble, R. A simple and efficient procedure for transformation of yeasts. BioTechniques 13, 18–20 (1992).

    Google Scholar 

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Hubl, S., Owens, J. & Nelson, H. Mutational analysis of the DNA-binding domain of yeast heat shock transcription factor. Nat Struct Mol Biol 1, 615–620 (1994). https://doi.org/10.1038/nsb0994-615

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