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Sequence-specific protein-DNA recognition by transcriptional regulatory proteins

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Abbreviations

HRE:

hormone response element

HTH:

helix-turn-helix

POU:

Pit, Oct, unc subfamily

References

  • Adams, T. H., M. T. Boylan and W. E. Timberlake. 1988.brlA is necessary and sufficient to direct conidiophore development inAspergillus nidulans. Cell 54: 353–362.

    Article  PubMed  CAS  Google Scholar 

  • Aggarwal, A. K., D. W. Rodgers, M. Drottar, M. Ptashne and S. C. Harrison. 1988. Recognition of a DNA operator by the repressor of phage 434: A view at high resolution. Science 242: 899–907.

    Article  PubMed  CAS  Google Scholar 

  • Akam, M. 1989.Hox and HOM: Homologous gene clusters in insects and vertebrates. Cell 57: 347–349.

    Article  PubMed  CAS  Google Scholar 

  • Anderson, W. F., D. H. Ohlendorf, Y. Takeda and B. W. Mathews. 1981. Structure of the Cro repressor from bacteriophage λ and its interaction with DNA. Nature 290: 754–758.

    Article  PubMed  CAS  Google Scholar 

  • Balling, R., U. Deutsch and P. Gruss. 1988.undulated, a mutation affecting the development of the mouse skeleton, has a point mutation in the paired box ofPax1. Cell 55: 531–535.

    Article  PubMed  CAS  Google Scholar 

  • Baumgartner, S., D. Bopp, M. Burri and M. Noll. 1987. Structure of two genes at thegooseberry locus related to thepaired gene and their spatial distribution. Genes and Devel. 1: 1247–1267.

    Article  CAS  Google Scholar 

  • Beato, M. 1989. Gene regulation by steroid hormones. Cell 56: 335–344.

    Article  PubMed  CAS  Google Scholar 

  • Berg, J. M. 1986. Potential metal-binding domains in nucleic acid binding proteins. Science 232: 485–487.

    Article  PubMed  CAS  Google Scholar 

  • Berg, J. M. 1988. Proposed structure for the zinc-binding domain from transcription factor IIIA and related proteins. Proc. Natl. Acad. Sci. USA 85: 99–102.

    Article  PubMed  CAS  Google Scholar 

  • Cohen, C. and D. A. D. Parry. 1986. α-Helical coiled coils—a widespread motif in proteins. Trends Biochem. Sci. 11: 245–248.

    Article  CAS  Google Scholar 

  • Costa, M., M. Weir, A., Coulson, J. Sulston and C. Kenyon. 1988. Posterior pattern formation inC. elegans involves position-specific expression of a gene containing a homeobox. Cell 55: 747–756.

    Article  PubMed  CAS  Google Scholar 

  • Crick, F.H.C. 1953. The, packing of α-helices: Simple coiled coils. Acta Cryst. 6: 689–697.

    Article  CAS  Google Scholar 

  • Curran, T. and B.R.J. Franza 1988. Fos and jun: The AP-1 connection. Cell 55: 395–397.

    Article  PubMed  CAS  Google Scholar 

  • Desplan, C., J. Theis and P. H. O'Farrell. 1988. The sequence specificity of homeodomain-DNA interactions. Cell 54: 1081–1090.

    Article  PubMed  CAS  Google Scholar 

  • Diakun, G. P., L. Fairall and A. Klug. 1986. EXAFS study of the zinc-binding sites in the protein transcription factor IIIA. Nature 324: 689–691.

    Article  Google Scholar 

  • Dodd, I. B. and J. B. Egan. 1987. Systematic method for, the detection of potential λ Crolike DNA-binding regions in proteins. J. Mol. Biol. 194: 557–564.

    Article  PubMed  CAS  Google Scholar 

  • Evans, R. M. 1988. The steroid and thyroid hormone receptor, superfamily. Science 240: 889–895.

    Article  PubMed  CAS  Google Scholar 

  • Evans, R. M. and S. M. Hollenberg. 1988. Zinc fingers: Gilt by association. Cell 52: 1–3

    Article  PubMed  CAS  Google Scholar 

  • Fairall, L., D. Rhodes and A. Klug. 1986. Mapping of the sites of protection, on a 5S RNA gene by theXenopus transcription factor IIIA: A model for the interaction. J. Mol. Biol. 192: 577–591.

    Article  PubMed  CAS  Google Scholar 

  • Fritz, A. F., K. W. Y. Cho, C. V. E. Wright, B. G. Jegalian and E. M. DeRobertis. 1989 Duplicated homeobox genes inXenopus. Dev. Biol. 131: 584–588.

    Article  PubMed  CAS  Google Scholar 

  • Gehring, W. J. and Y. Hiromi. 1986. Homeotic genes and the homeobox. Ann. Rev. Genet. 20: 147–173.

    Article  PubMed  CAS  Google Scholar 

  • Gentz, R. and F. J. Rauscher III. 1989. Parallel association of Fos and Jun leucine zippers juxtaposes DNA-binding domains. Science 243: 1695–1699.

    Article  PubMed  CAS  Google Scholar 

  • Graham, A., N. Papalopulu and R. Krumlauf. 1989. The murine andDrosophila homeobox gene complexes have common features of organization, and expression. Cell 57: 367–378.

    Article  PubMed  CAS  Google Scholar 

  • Gralla, J. D. 1989. Bacterial gene regulation from distant DNA sites. Cell 57: 193–195.

    Article  PubMed  CAS  Google Scholar 

  • Green, S., and P. Chambon. 1988. Nuclear receptors enhance our understanding of transcription regulation. Trends Genet. 4: 309–314.

    Article  PubMed  CAS  Google Scholar 

  • Han, K., M. S. Levine and J. L. Manley. 1989. Synergistic activation and repression of transcription byDrosophila homeobox proteins. Cell 56: 573–583.

    Article  PubMed  CAS  Google Scholar 

  • Helmann, J. D. and M. J. Chamberlin. 1988. Structure and function of bacterial sigma factors. Ann. Rev. Biochem. 57: 839–872.

    Article  PubMed  CAS  Google Scholar 

  • Herr, W., R. A. Sturm, R. G. Clerc, L. M. Corcoran, D. Baltimore, P. A. Sharp, H. A. Ingraham, M. G. Rosenfeld, M. Finney, G. Ruvkun and H. R. Horvitz. 1988. The POU domain: A large conserved region in the mammalianpit-1, oct-1, oct-2, andCaenorhabditis elegans unc-86 gene products. Genes and Devel. 2: 1513–1516.

    Article  CAS  Google Scholar 

  • Hodges, R. S., P. D. Semchuk, A. K. Taneja, C. M. Kay, J. M. R. Parker and C. T. Mant. 1988. Protein design using model synthetic peptides. Peptide Res. 1: 19–30.

    CAS  Google Scholar 

  • Hoeffler, J. P., T. E. Meyer, Y. Yungdae, J. L. Jameson and J. F. Habener. 1988. Cyclic AMP-responsive DNA-binding protein: structure based on a cloned placental cDNA. Science 242: 1430–1433.

    Article  PubMed  CAS  Google Scholar 

  • Jaynes, J. B. and P. H. O'Farrell. 1988. Activation and repression of transcription by homeodomain-containing proteins that bind a common site. Nature 336: 744–749.

    Article  PubMed  CAS  Google Scholar 

  • Johnson, P. F. and S. L. McKnight. 1989. Ann. Rev. Biochem. 58: 799.

    Article  PubMed  CAS  Google Scholar 

  • Johnston, M. 1987. Geneticevidence that zinc is an essential, co-factor in the DNA-binding domain of GAL4 protein. Nature 328: 353–355.

    Article  PubMed  CAS  Google Scholar 

  • Jordan, S. R. and C. O. Pabo. 1988. Structure of the lambda complex at 2.5 Å resolution: Details of the repressor-operator interactions. Science 242: 893–899.

    Article  PubMed  CAS  Google Scholar 

  • Klug, A. and D. Rhodes, 1987. ‘Zinc fingers’: A novel protein motif for nucleic acid recognition. Trends Biochem. Sci. 12:464–469.

    Article  CAS  Google Scholar 

  • Ko, H. S., P. Fast, W. McBride and L. M. Staudt. 1988. A human protein specific for the immunoglobulin octamer DNA motif contains a functional homeobox domain. Cell 55: 135–144.

    Article  PubMed  CAS  Google Scholar 

  • Kouzarides, T. and E. Ziff. 1988. The role of the leucine zipper in the fos-jun interaction. Nature 336: 646–647.

    Article  PubMed  CAS  Google Scholar 

  • Landschultz, W. H., P. F. Johnson and S. L. McKnight. 1988. The leucine zipper: A hypothetical structure common to a new class of DNA-binding proteins. Science 240: 1759–1764.

    Article  Google Scholar 

  • Landschultz, W. H., P. F. Johnson and S. L. McKnight. 1989. The DNA-binding domain of the rat liver nuclear protein C/EBP is bipartite. Science 243: 1681–1688.

    Article  Google Scholar 

  • Laughon, A. and M. P. Scott. 1984. Sequence of aDrosophila segmentation gene: protein structure homology with DNA-binding proteins. Nature 310: 25–31.

    Article  PubMed  CAS  Google Scholar 

  • Lesczynski, J. F. and G. D. Rose. 1986. Loops in globular proteins: A novel category of secondary structure. Science 234: 849–855.

    Article  Google Scholar 

  • Levine, M. and T. Hoey. 1988. Homeobox proteins as sequence-specific transcription factors. Cell 55: 537–540.

    Article  PubMed  CAS  Google Scholar 

  • Mardon, G. and D. C. Page. 1989. The sex-determining region of the mouse Y chromosome encodes a protein with a highly acidic domain and 13 zinc fingers. Cell 56: 765–770.

    Article  PubMed  CAS  Google Scholar 

  • Mathews, B. 1988. No code for recognition. Nature 335: 294–295.

    Article  Google Scholar 

  • McClarin, J. A., C. A. Frederick, B. C. Wang, P. Greene, H. W. Boyer, J. Grable and J. M. Rosenberg. 1988. Structure of the DNA-EcoR1 endonuclease recognition complex at 3 Å resolution. Science 234: 1526–1541.

    Article  Google Scholar 

  • Miller, J., A. D. McLachlan and A. Klug. 1985. Repetitive zinc-binding domains in the protein transcription factor IIIA fromXenopus oocytes. EMBO J. 4: 1609–1614.

    PubMed  CAS  Google Scholar 

  • Muller, M., M. Affolter, W. Leupin, G. Otting, K. Wutrich and W. J. Gehring. 1988. Isolation and sequence-specific DNA binding of theAntennapedia homeodomain. EMBO J. 7: 4299–4304.

    PubMed  CAS  Google Scholar 

  • Murre, C., P. S. McCaw and D. Baltimore. 1989. A new DNA binding and dimerization motif in immunoglobulin enhancer binding,daughterless, MyoD, andmyc proteins. Cell 56: 777–783.

    Article  PubMed  CAS  Google Scholar 

  • O'Shea, E. K., R. Rutkowski and P. S. Kim. 1989. Evidence that the leucine zipper is a coiled coil. Science 243: 538–542.

    Article  PubMed  Google Scholar 

  • Ollis, D. L. and S. W. White. 1987. Structural basis of protein-nucleic acid interactions. Chem. Rev. 87: 981–995.

    Article  CAS  Google Scholar 

  • Otting, G., Y. Qian, M. Muller, M. Affolter, W. Gehring and K. Wutrich. 1988. Secondary structure determination for the Antennapedia homeodomain by nuclear magnetic resonance and evidence for a helix-turn-helix. EMBO J. 7: 4305–4309.

    PubMed  CAS  Google Scholar 

  • Otwinowski, Z., R. W. Schevitz, R. G. Zhang, C. L. Lawson, A. Joachimiak, R. Q. Marmorstein, B. F. Luisi and P. B. Sigler. 1988. Crystal structure oftrp repressor/operator complex at atomic resolution. 335: 321–329.

    CAS  Google Scholar 

  • Pabo, C. O. and R. T. Sauer. 1984. Protein-DNA recognition. Ann. Rev. Biochem. 53: 293–321.

    Article  PubMed  CAS  Google Scholar 

  • Parkhurst, S. M., D. A. Harrison, M. P. Remington, C. Spava, R. L. Kelley, R. S. Coyne and V. G. Corces. 1988. TheDrosophila su(Hw) gene, which controls the phenotypic effect of the gypsy transposable element, encodes a putative DNA-binding protein. Genes and Devel. 2: 1205–1215.

    Article  CAS  Google Scholar 

  • Parraga, G., S. J. Horvath, A. Eisen, W. E. Taylor, L. Hood, E. T. Young and R. E. Klevitt. 1988. Zinc-dependent structure of a single-finger domain. Science 241: 1489–1492.

    Article  PubMed  CAS  Google Scholar 

  • Pfeifer, K., K. S. Kim, S. Kogan and L. Guarente. 1989. Functional dissection and sequence of yeast HAP1 activator. Cell 56: 291–301.

    Article  PubMed  CAS  Google Scholar 

  • Pruss, G. J. and K. Drlica. 1989. DNA supercoiling and prokaryotic transcription. Cell 56: 521–523.

    Article  PubMed  CAS  Google Scholar 

  • Ptashne, M. 1988. How eukaryotic transcriptional activators work. Nature 335: 683–689.

    Article  PubMed  CAS  Google Scholar 

  • Rhodes, D. and A. Klug. 1986. An underlying repeat in some transcriptional control sequences corresponding to half a double helical turn of DNA. Cell 46: 123–132.

    Article  PubMed  CAS  Google Scholar 

  • Rosenberg, J. M., J. A. McClarin, C. A. Frederick, B. C. Wang, J. Grable, H. W. Boyer and P. Greene. 1987. Structure and recognition mechanism of EcoR1 endonuclease. Trends Biochem. Sci. 12: 395–398.

    Article  CAS  Google Scholar 

  • Saenger, W.. 1984. Principles of nucleic acid structure. Springer-Verlag, New York

    Google Scholar 

  • Schlief, R.. 1988. DNA binding by proteins. Science 241: 1182–1187.

    Article  Google Scholar 

  • Seeman, N. C., J. M. Rosenberg and A. Rich. 1976. Sequence-specific recognition of double helical nucleic acids by proteins. Proc. Natl. Acad. Sci. USA 73: 804–808.

    Article  PubMed  CAS  Google Scholar 

  • Sigler, P. B.. 1988. Acid blobs and negative noddles. Nature 333: 683–689.

    Article  Google Scholar 

  • Steitz, T. and I. Weber. 1985. Structure of catabolite gene activator protein.In Biological Macromolecules and Assemblies (F. Jurnak and A. McPherson, ed.) John Wiley and Sons, New York.

    Google Scholar 

  • Struhl, K.. 1989. Helix-turn-helix, zinc-finger, and leucine-zipper motifs for eukaryotic transcriptional regulatory proteins. Trends Biochem. Sci. 14: 137–140.

    Article  PubMed  CAS  Google Scholar 

  • Tomlinson, A., B. E. Kimmel and G. M. Rubin. 1988.rough, aDrosophila homeobox gene required in photoreceptors R2 and R5 for inductive interactions in the developing eye. Cell 55: 771–784.

    Article  PubMed  CAS  Google Scholar 

  • Tso, J. Y., D. J. Van Den Berg and L. J. Korn. 1986. Structure of the gene forXenopus transcription factor IIIA. Nucleic Acids Res. 14: 2187–2200.

    Article  PubMed  CAS  Google Scholar 

  • Turner, R. and R. Tjian. 1989. Leucine repeats and an adjacent DNA-binding domain mediate the formation of functional cFos-cJun heterodimers. Science 243: 1689–1694.

    Article  PubMed  CAS  Google Scholar 

  • Wang, J. C. and G. N. Giaever. 1988. Action at a distance along a DNA. Science 240: 300–304.

    Article  PubMed  CAS  Google Scholar 

  • Way, J. C. and M. Chalfie. 1988.mec-3, a homeobox-containing gene that specifies differentiation of the touch receptor neurons inC. elegans. Cell 54: 5–16.

    Article  PubMed  CAS  Google Scholar 

  • Wiederrecht, G., D. Seto and C. S. Parker. 1988. Isolation of the gene encoding theS. cerevisiae heat shock transcription factor. Cell 54: 841–853.

    Article  PubMed  CAS  Google Scholar 

  • Wolberger, C., Y. Dong, M. Ptashne and S. C. Harrison. 1988. Structure of a phage 434 Cro/DNA complex. Nature 335: 789–795.

    Article  PubMed  CAS  Google Scholar 

  • Wright, C. V. E., K. W. Y. Cho, G. Oliver and E. M. DeRobertis. 1989a. Vertebrate homeodomain proteins: Families of region-specific transcription factors. Trends Biochem. Sci. 14: 52–56.

    Article  PubMed  CAS  Google Scholar 

  • Wright, W. E., D. A. Sassoon and V. K. Lin. 1989b. Myogenin, a factor regulating myogenesis, has a domain homologous to MyoD. Cell 56: 607–617.

    Article  PubMed  CAS  Google Scholar 

  • Yaniv, M. and S. Cereghini. 1986. Structure of transcriptionally active chromatin. Crit. Rev. Biochem. 21: 1–26.

    CAS  Google Scholar 

  • Zhang, R.g., A. Joachimiak, C. L. Lawson, R. W. Schevitz, Z. Otwinowski and P. B. Sigler. 1987. The crystal structure oftrp aporepressor at 1.8 Å shows how binding of tryptophan enhances DNA affinity. Nature 327: 591–597.

    Article  PubMed  CAS  Google Scholar 

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  1. Department of Biochemistry, The University of Georgia, 30602, Athens, Georgia

    Claiborne V. C. Glover

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Glover, C.V.C. Sequence-specific protein-DNA recognition by transcriptional regulatory proteins. Plant Mol Biol Rep 7, 183–208 (1989). https://doi.org/10.1007/BF02668686

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