Linker length and composition influence the flexibility of Oct-1 DNA binding

EMBO Journal

Volumn 16, Issue 8, 1997, Pages 2043-2053

  Van Leeuwen, Hans C ^a   Strating, Marijke J ^a   Rensen, Marije ^a   De Laat, Wouter ^b   Van Der Vliet, Peter C ^a  

^a UTRECHT UNIVERSITY   (Netherlands)

^b ERASMUS MEDICAL CENTER   (Netherlands)

Author keywords

DNA binding; Linker region; Octamer site; POU proteins

Indexed keywords

GLUTAMIC ACID; HELIX LOOP HELIX PROTEIN; TRANSCRIPTION FACTOR;

AMINO ACID SEQUENCE; ARTICLE; BINDING AFFINITY; BINDING SITE; COMPUTER MODEL; CONTROLLED STUDY; DNA BINDING; DNA FOOTPRINTING; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN DOMAIN; PROTEIN STRUCTURE;

AMINO ACID SEQUENCE; BASE SEQUENCE; DNA FOOTPRINTING; DNA-BINDING PROTEINS; GLUTAMIC ACID; HELIX-TURN-HELIX MOTIFS; HOMEODOMAIN PROTEINS; HOST CELL FACTOR C1; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; OCTAMER TRANSCRIPTION FACTOR-1; PROTEIN CONFORMATION; SEQUENCE DELETION; TRANSCRIPTION FACTORS;

EID: 0030937754     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/16.8.2043     Document Type: Article

References (39)

1. Andres, V., Chiara, M.D. and Mahdavi, V. (1994) A new bipartite DNA-binding domain: cooperative interaction between the cut repeat and homeo domain of the cut homeo proteins. Genes Dev., 8, 245-257.
2. Assa-Munt, N., Mortishire-Smith, R.J., Aurora, R., Herr, W. and Wright, P.E. (1993) The solution structure of the Oct-1 POU-specific domain reveals a striking similarity to the bacteriophage λ repressor DNA binding domain. Cell, 73, 193-205.
3. Aurora, R. and Herr, W. (1992) Segments of the POU domain influence one another's DNA-binding specificity. Mol. Cell. Biol., 12, 455-467.
4. Botfield, M.C., Jansco, A. and Weiss, M.A. (1992) Biochemical characterization of the Oct-2 POU domain with implications for bipartite DNA recognition. Biochemistry, 31, 5841-5848.
5. Botfield, M.C. Jansco, A. and Weiss, M.A. (1994) An invariant asparagine in the POU-specific homeodomain regulates the specificity of the Oct-2 POU motif. Biochemistry, 33, 8113-8121.
6. Certel, K., Anderson, M.G., Shrigley, R. and Johnson, W.A. (1996) Distinct variant DNA-binding sites determine cell-specific autoregulated expression of the Drosophila POU domain transcription factor Drifter in midline glia or trachea. Mol. Cell. Biol., 16, 1813-1823.
7. Cleary, M.A. and Herr, W. (1995) Mechanisms for flexibility in DNA sequence recognition and VP16-induced complex formation by the Oct-1 POU domain. Mol. Cell. Biol., 15, 2090-2100.
8. Cox, M. van Tilborg, P.J., de Laat, W., Boelens, R., van Leeuwen, H.C., van der Vliet, P.C. and Kaptein, R. (1995) Solution structure of the Oct-1 POU homeodomain determined by NMR and restrained molecular dynamics. J. Biomol. NMR, 6, 23-32.
9. Dekker, N., Cox, M., Boelens, R., Verrijzer, C.P., van der Vliet, P.C. and Kaptein, R. (1993) Solution structure of the POU-specific DNA-binding domain of Oct-1. Nature, 362, 852-855.
10. Greenstein, D., Hird, S., Plasterk, R.H., Andachi, Y., Kohara, Y., Wang, B., Finney, M. and Ruvkun, G. (1994) Targeted mutations in the Caenorhabditis elegans POU homeo box gene ceh-18 cause defects in oocyte cell cycle arrest, gonad migration, and epidermal differentiation. Genes Dev., 8, 1935-1948.
11. Gstaiger, M., Knoepfel, L., Georgiev, O., Schaffner, W. and Hovens, C.M. (1995) A B-cell coactivator of octamer-binding transcription factors. Nature, 373, 360-362.
12. Gstaiger, M., Georgiev, O., van Leeuwen, H., van der Vliet, P. and Schaffner, W. (1996) The B cell coactivator Bob1 shows DNA sequence-dependent complex formation with Oct-1/Oct-2 factors, leading to differential promoter activation. EMBO J., 15, 2781-2790.
13. Herr, W. and Cleary, M.A. (1995) The POU domain: versatility in transcriptional regulation by a flexible two-in-one DNA-binding domain. Genes Dev., 9, 1679-1693.
14. Ingraham, H.A., Chen, R.P., Mangalam, H.J., Elsholtz, H.P., Flynn, S.E., Lin, C.R., Simmons, D.M., Swanson, L. and Rosenfeld, M.G. (1988) A tissue-specific transcription factor containing a homeodomain specifies a pituitary phenotype. Cell, 55, 519-529.
15. Jin, Y., Mead, J., Li, T., Wolberger, C. and Vershon, A.K. (1995) Altered DNA recognition and bending by insertions in the alpha 2 tail of the yeast a1/alpha 2 homeodomain heterodimer. Science, 270, 290-293.
16. Klemm, J.D. and Pabo, C.O. (1996) Oct-1 POU domain-DNA interactions: cooperative binding of isolated subdomains and effects of covalent linkage. Genes Dev., 10, 27-36.
17. Klemm, J.D., Rould, M.A., Aurora, R., Herr, W. and Pabo, C.O. (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.
18. Kraulis, P.J. (1991) Molscript: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr., 24, 946-950.
19. Lai, J.S., Cleary, M.A. and Herr, W. (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.
20. Li, P., He, X., Gerrero, M.R., Mok, M., Aggarwal, A. and Rosenfeld, M.G. (1993) Spacing and orientation of bipartite DNA-binding motifs as potential functional determinants for POU domain factors. Genes Dev., 7, 2483-2496.
21. Li, T., Stark, M.R., Johnson, A.D. and Wolberger, C. (1995) Crystal structure of the MATa1/MAT alpha 2 homeodomain heterodimer bound to DNA. Science, 270, 262-269.
22. Liang, J., Moye-Rowley, S. and Maurer, R.A. (1995) In vivo mutational analysis of the DNA binding domain of the tissue specific transcription factor, Pit-1. J. Biol. Chem., 270, 25520-25525.
23. Luo, Y. and Roeder, R.G. (1995) Cloning, functional characterization, and mechanism of action of the B-cell-specific transcriptional coactivator OCA-B. Mol. Cell. Biol., 15, 4115-4124.
24. Matsuo, K., Clay, O., Künzler, P., Georgiev, O., Urbánek, P. and Schaffner, W. (1994) Short intron interrupting the Oct-2 POU domain may prevent recombination between POU family genes without interfering with potential POU domain 'shuffling' in evolution. Biol. Chem. Hoppe-Seyler, 375, 675-683.
25. Ogata, K., Morikawa, S., Nakamura, H., Sekikawa, A., Inoue, T., Kanai, H., Sarai, A., Ishii, S. and Nishimura, Y. (1994) Solution structure of a specific DNA complex of the Myb DNA-binding domain with cooperative recognition helices. Cell, 79, 639-648.
26. O'Shannessy, D.J., Brigham-Burke, M., Soneson, K.K., Hensley, P. and Brooks, I. (1993) Determination of rate and equilibrium binding constants for macromolecular interactions using surface plasmon resonance: use of nonlinear least square analysis methods. Anal. Biochem., 212, 457-468.
27. Pavletich, N.P. and Pabo, C.O. (1993) Crystal structure of a five-finger GLI-DNA complex: new perspectives on zinc fingers. Science, 261, 1701-7.
28. Pomerantz, J.L., Kristie, T.M. and Sharp, P.A. (1992) Recognition of the surface of a homeo domain protein. Genes Dev., 6, 2047-2057.
29. Pomerantz, J.L., Sharp, P.A. and Pabo, C.O. (1995) Structure-based design ot transcription factors. Science, 267, 93-96.
30. Schöler, H.R. (1991) Octamania: the POU factors in murine development. Trends Genet., 7, 323-329.
31. Strubin, M., Newell, J.W. and Matthias, P. (1995) OBF-1, a novel B cell-specific coactivator that stimulates immunoglobulin promoter activity through association with octamer-binding proteins. Cell, 80, 497-506.
32. Studier, W.F., Rosenberg, A.H., Dunn, J.J. and Dubendorf, J.W. (1990) Use of T7 RNA polymerase to direct expression of cloned genes. Methods Enzymol., 185, 60-89.
33. Sturm, R.A., Cassady, J.L., Das, G., Romo, A. and Evans, G.A. (1993) Chromosomal structure and expression of the human OTF1 locus encoding the Oct-1 protein. Genomics, 16, 333-341.
34. van Leeuwen, H.C., Strating, M.J., Cox, M., Kaptein, R. and van der Vliet, P.C. (1995) Mutation of the Oct-1 POU-specific recognition helix leads to altered DNA binding and influences enhancement of adenovirus DNA replication. Nucleic Acids Res., 23, 3189-3197.
35. Verrijzer, C.P., Kal, A.J. and Van der Vliet, P.C. (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.
36. Verrijzer, C.P., Alkema, M.J., van Weeperen, W.W., van Leeuwen, H.C., Strating, M.J.J. and van der Vliet, P.C. (1992a) The DNA-binding specificity of the bipartite POU domain and its subdomains. EMBO J., 11, 4993-5002.
37. Verrijzer, C.P., van Oosterhout, J.A.W.M., van Weperen, W.W. and van der Vliet, P.C. (1992b) POU proteins bend DNA via the POU-specific domain. EMBO J., 10, 3007-3014.
38. Verrijzer, P.C., Strating, M.J.J., Mul, Y.M. and van der Vliet, P.C. (1992c) POU domain transcription factors from different subclasses stimulate adenovirus DNA replication. Nucleic Acids Res., 20, 6369-6375.
39. Walker, S., Hayes, S. and O'Hare, P. (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.