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Research Article

Mechanisms for Flexibility in DNA Sequence Recognition and VP16-Induced Complex Formation by the Oct-1 POU Domain

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Pages 2090-2100 | Received 31 Oct 1994, Accepted 05 Jan 1995, Published online: 30 Mar 2023

REFERENCES

  • apRhys, C. M., D. M. Ciufo, E. A. O'Neill, T. J. Kelly, and G. S. Hayward. 1989. Overlapping octamer and TAAGARAT motifs in the VF65-response elements in the herpes simplex virus immediate-early promoters represent independent binding sites for cellular nuclear factor III. J. Virol. 63:2798–2812.
  • Assa-Munt, N., R. J. Mortishire-Smith, R. Aurora, W. Herr, and P. E. Wright. 1993. The solution structure of the Oct-1 POU-specific domain reveals a striking similarity to the bacteriophage l DNA-binding domain. Cell 73:193–205.
  • Aurora, R. 1992. Ph.D. thesis. State University of New York, Stony Brook.
  • Aurora, R., and W. Herr. 1992. Segments of the POU domain influence one another's DNA-binding specificity. Mol. Cell. Biol. 12:455–467.
  • Baumruker, T., R. Sturm, and W. Herr. 1988. OBP100 binds remarkably degenerate octamer motifs through specific interactions with flanking sequences. Genes Dev. 2:1400–1413.
  • Botfield, M. C., A. Jansco, and M. A. Weiss. 1992. Biochemical characterization of the Oct-2 POU domain with implications for bipartite DNA recognition. Biochemistry 31:5841–5848.
  • Botfield, M. C., A. Jansco, and M. A. Weiss. 1994. Mapping critical residues in eukaryotic DNA-binding proteins: a plasmid-based genetic selection strategy with application to the Oct-2 POU motif. Biochemistry 33:6177–6185.
  • Cleary, M., and W. Herr. Unpublished data.
  • Cleary, M. A., S. Stern, M. Tanaka, and W. Herr. 1993. Differential positive control by Oct-1 and Oct-2: activation of a transcriptionally silent motif through Oct-1 and VP16 corecruitment. Genes Dev. 7:72–83.
  • Dekker, N., M. Cox, R. Boelens, C. P. Verrijzer, P. C. van der Vliet, and R. Kaptein. 1993. Solution structure of the POU-specific DNA-binding domain of Oct-1. Nature (London) 362:852–855.
  • Ebright, R. H. 1991. Identification of amino-acid–base pair contacts by genetic methods. Methods Enzymol. 208:620–640.
  • Gerster, T., and R. G. Roeder. 1988. A herpesvirus trans-activating protein interacts with transcription factor OTF-1 and other cellular proteins. Proc. Natl. Acad. Sci. USA 85:6347–6351.
  • Herr, W. 1992. Oct-1 and Oct-2: differential transcriptional regulation by proteins that bind to the same DNA sequence, p. 1103–1135. In S. L. McKnight, and K. Yamamoto (ed.), Transcriptional regulation. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
  • 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 mammalian pit-1, oct-1, oct-2, and Caenorhabditis elegans unc-86 gene products. Genes Dev. 2:1513–1516.
  • Ingraham, H. A., S. E. Flynn, J. W. Voss, V. R. Albert, M. S. Kapiloff, L. Wilson, and M. G. Rosenfeld. 1990. The POU-specific domain of Pit-1 is essential for sequence-specific, high affinity DNA binding and DNA-dependent Pit-1–Pit-1 interactions. Cell 61:1021–1033.
  • Jansco, A., M. C. Botfield, L. C. Sowers, and M. A. Weiss. 1994. An altered-specificity mutation in a human POU domain demonstrates functional analogy between the POU-specific subdomain and phage l repressor. Proc. Natl. Acad. Sci. USA 91:3887–3891.
  • Klemm, J. D., M. A. Rould, R. Aurora, W. Herr, and C. O. Pabo. 1994. Crystal structure of the Oct-1 POU domain bound to an octamer site: DNA recognition with tethered DNA-binding modules. Cell 77:21–32.
  • Kristie, T. M., J. H. LeBowitz, and P. A. Sharp. 1989. The octamer-binding proteins form multi-protein–DNA complexes with the HSV αTIF regulatory protein. EMBO J. 8:4229–4238.
  • Kristie, T. M., and P. A. Sharp. 1990. Interactions of the Oct-1 POU sub-domains with specific DNA sequences and with the HSV α-trans-activator protein. Genes Dev. 4:2383–2396.
  • Kunkel, T. A., J. D. Roberts, and R. A. Zakour. 1987. Rapid and efficient site-specific mutagenesis without phenotypic selection. Methods Enzymol. 154:367–382.
  • Lai, J.-S., M. A. Cleary, and W. Herr. 1992. A single amino acid exchange transfers VP16-induced positive control from the Oct-1 to the Oct-2 homeo domain. Genes Dev. 6:2058–2065.
  • Li, P., X. He, M. R. Gerrero, M. Mok, A. Aggarwal, and M. G. Rosenfeld. 1993. Spacing and orientation of bipartite DNA-binding motifs as potential functional determinants for POU domain factors. Genes Dev. 7:2483–2496.
  • O'Hare, P., and C. R. Goding. 1988. Herpes simplex virus regulatory elements and the immunoglobulin octamer domain bind a common factor and are both targets for virion transactivation. Cell 52:435–445.
  • O'Hare, P., C. R. Goding, and A. Haigh. 1988. Direct combinatorial interaction between a herpes simplex virus regulatory protein and a cellular octamer-binding factor mediates specific induction of virus immediate early gene expression. EMBO J. 7:4231–4238.
  • Pabo, C. O., A. K. Aggarwal, S. R. Jordan, L. J. Beamer, U. R. Obeysekare, and S. C. Harrison. 1990. Conserved residues make similar contacts in two repressor–operator complexes. Science 247:1210–1213.
  • Pfaffle, R. W., G. E. DiMattia, J. S. Parks, M. R. Brown, J. M. Wit, M. Jansen, H. Van der Nat, J. L. Van den Brande, M. G. Rosenfeld, and H. A. Ingraham. 1992. Mutation of the POU-specific domain of Pit-1 and hypo-pituitarism without pituitary hypoplasia. Science 257:1118–1121.
  • Pomerantz, J. L., T. M. Kristie, and P. A. Sharp. 1992. Recognition of the surface of a homeo domain protein. Genes Dev. 6:2047–2057.
  • Preston, C. M., M. C. Frame, and M. E. M. Campbell. 1988. A complex formed between cell components and an HSV structural polypeptide binds to a viral immediate early gene regulatory DNA sequence. Cell 52:425–434.
  • Pruijn, G. J. M., W. van Driel, R. T. van Miltenburg, and P. C. van der Vliet. 1987. Promoter and enhancer elements containing a conserved sequence motif are recognized by nuclear factor III, a protein stimulating adenovirus DNA replication. EMBO J. 6:3771–3778.
  • Rodgers, D. W., and S. C. Harrison. 1993. The complex between phage 434 repressor DNA-binding domain and operator sites OR3: structural differences between consensus and non-consensus half-sites. Structure 1:227–240.
  • Sanger, F., S. Nicklen, and A. R. Coulson. 1977. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 74:5463–5467.
  • Sivaraja, M., M. C. Botfield, M. Mueller, A. Jansco, and M. A. Weiss. 1994. 3D-NMR studies of human B-cell transcription factor Oct-2. Biochemistry 33:9845–9855.
  • Stern, S., and W. Herr. 1991. The herpes simplex virus trans-activator VP16 recognizes the Oct-1 homeo domain: evidence for a homeo domain recognition subdomain. Genes Dev. 5:2555–2566.
  • Stern, S., M. Tanaka, and W. Herr. 1989. The Oct-1 homeodomain directs formation of a multiprotein–DNA complex with the HSV transactivator VP16. Nature (London) 341:624–630.
  • Studier, F. W., A. H. Rosenberg, J. J. Dunn, and J. W. Dubendorff. 1990. Use of T7 RNA polymerase to direct expression of cloned genes. Methods En-zymol. 185:60–89.
  • Sturm, R. A., T. Baumruker, B. R. Franza, Jr., and W. Herr. 1987. A 100-kD HeLa cell octamer binding protein (OBP100) interacts differently with two separate octamer-related sequences within the SV40 enhancer. Genes Dev. 1:1147–1160.
  • Sturm, R. A., and W. Herr. 1988. The POU domain is a bipartite DNA-binding structure. Nature (London) 336:601–604.
  • Tanaka, M., U. Grossniklaus, W. Herr, and N. Hernandez. 1988. Activation of the U2 snRNA promoter by the octamer motif defines a new class of RNA polymerase II enhancer elements. Genes Dev. 2:1764–1778.
  • Thompson, C. C., and S. L. McKnight. 1992. Anatomy of an enhancer. Trends Genet. 8:232–236.
  • Verrijzer, C. P., M. J. Alkema, W. W. van Weperen, H. C. van Leeuwen, M. J. J. Strating, and P. C. van der Vliet. 1992. The DNA binding specificity of the bipartite POU domain and its subdomains. EMBO J. 11:4993–5003.
  • Verrijzer, C. P., A. J. Kal, and P. C. van der Vliet. 1990. The oct-1 homeo domain contacts only part of the octamer sequence and full oct-1 DNA binding activity requires the POU-specific domain. Genes Dev. 4:1964–1974.
  • Walker, S., S. Hayes, and P. O'Hare. 1994. Site-specific conformational alteration of the Oct-1 POU domain-DNA complex as the basis for differential recognition by Vmw65 (VP16). Cell 79:841–852.
  • Xiao, P., and J. P. Capone. 1990. A cellular factor binds to the herpes simplex virus type 1 trans-activator Vmw65 and is required for Vmw65-dependent protein-DNA complex assembly with Oct-1. Mol. Cell. Biol. 10:4974–4977.
  • Zoller, M. J., and M. Smith. 1983. Oligonucleotide-directed mutagenesis of DNA fragments cloned into M13 vectors. Methods Enzymol. 100:468–500.

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