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. 1996 Aug;16(8):4404–4413. doi: 10.1128/mcb.16.8.4404

Conformational alteration of Oct-1 upon DNA binding dictates selectivity in differential interactions with related transcriptional coactivators.

V Misra 1, S Walter 1, P Yang 1, S Hayes 1, P O'Hare 1
PMCID: PMC231439  PMID: 8754841

Abstract

VP16 (termed VP16-H here) of herpes simplex virus (HSV) belongs to a family of related regulatory proteins which includes VP16-B of bovine herpesvirus (BHV). We show that VP16-B, while also being a powerful transactivator of transcription dependent on Oct-1 binding sites in its target promoters, has virtually no activity on a defined VP16-H-responsive, octamer-containing target promoter. While Oct-1 binds equally well to the VP16-B-responsive and -nonresponsive sites, VP16-B interacts with Oct-1 only when Oct-1 is bound to the BHV octamer site and not when it is bound to the HSV site. We show from the analysis of chimeric proteins that the ability of VP16-B to discriminate between the Oct-1 forms depends on features of its N-terminal region. We also show from an analysis of chimeric DNA motifs that sequences that lie 3' to the POU domain-contacting region of the HSV octamer site play a role in making it unresponsive to VP16-B. Finally, we show by high-resolution hydroxyl radical footprint analysis that the conformation of Oct-l is different on the two sites. These results augment our previous report on an allosteric effect of DNA signals on the conformation of bound proteins and indicate that different conformations of the same DNA binding protein can be recognized selectively by related members of interacting regulatory proteins. The possible implications of our observations for selective gene regulation by Oct-1, a ubiquitous transcription factor, and other multimember transcription families are discussed.

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Selected References

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  1. Carbon P., Murgo S., Ebel J. P., Krol A., Tebb G., Mattaj L. W. A common octamer motif binding protein is involved in the transcription of U6 snRNA by RNA polymerase III and U2 snRNA by RNA polymerase II. Cell. 1987 Oct 9;51(1):71–79. doi: 10.1016/0092-8674(87)90011-0. [DOI] [PubMed] [Google Scholar]
  2. Carpenter D. E., Misra V. Sequences of the bovine herpesvirus 1 homologue of herpes simplex virus type-1 alpha-trans-inducing factor (UL48). Gene. 1992 Oct 1;119(2):259–263. doi: 10.1016/0378-1119(92)90280-3. [DOI] [PubMed] [Google Scholar]
  3. Cheung C. H., Fan Q. N., Stumph W. E. Structural requirements for the functional activity of a U1 snRNA gene enhancer. Nucleic Acids Res. 1993 Jan 25;21(2):281–287. doi: 10.1093/nar/21.2.281. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Cleary M. A., Herr W. Mechanisms for flexibility in DNA sequence recognition and VP16-induced complex formation by the Oct-1 POU domain. Mol Cell Biol. 1995 Apr;15(4):2090–2100. doi: 10.1128/mcb.15.4.2090. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Dailey L., Yuan H., Basilico C. Interaction between a novel F9-specific factor and octamer-binding proteins is required for cell-type-restricted activity of the fibroblast growth factor 4 enhancer. Mol Cell Biol. 1994 Dec;14(12):7758–7769. doi: 10.1128/mcb.14.12.7758. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Davison A. J., Scott J. E. The complete DNA sequence of varicella-zoster virus. J Gen Virol. 1986 Sep;67(Pt 9):1759–1816. doi: 10.1099/0022-1317-67-9-1759. [DOI] [PubMed] [Google Scholar]
  7. Elliott G., O'Hare P. Equine herpesvirus 1 gene 12, the functional homologue of herpes simplex virus VP16, transactivates via octamer sequences in the equine herpesvirus IE gene promoter. Virology. 1995 Oct 20;213(1):258–262. doi: 10.1006/viro.1995.1568. [DOI] [PubMed] [Google Scholar]
  8. Falkner F. G., Zachau H. G. Correct transcription of an immunoglobulin kappa gene requires an upstream fragment containing conserved sequence elements. Nature. 1984 Jul 5;310(5972):71–74. doi: 10.1038/310071a0. [DOI] [PubMed] [Google Scholar]
  9. Gerster T., Roeder R. G. A herpesvirus trans-activating protein interacts with transcription factor OTF-1 and other cellular proteins. Proc Natl Acad Sci U S A. 1988 Sep;85(17):6347–6351. doi: 10.1073/pnas.85.17.6347. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Greaves R. F., O'Hare P. Structural requirements in the herpes simplex virus type 1 transactivator Vmw65 for interaction with the cellular octamer-binding protein and target TAATGARAT sequences. J Virol. 1990 Jun;64(6):2716–2724. doi: 10.1128/jvi.64.6.2716-2724.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Greaves R., O'Hare P. Separation of requirements for protein-DNA complex assembly from those for functional activity in the herpes simplex virus regulatory protein Vmw65. J Virol. 1989 Apr;63(4):1641–1650. doi: 10.1128/jvi.63.4.1641-1650.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Groenen M. A., Dijkhof R. J., van der Poel J. J., van Diggelen R., Verstege E. Multiple octamer binding sites in the promoter region of the bovine alpha s2-casein gene. Nucleic Acids Res. 1992 Aug 25;20(16):4311–4318. doi: 10.1093/nar/20.16.4311. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Gstaiger M., Knoepfel L., Georgiev O., Schaffner W., Hovens C. M. A B-cell coactivator of octamer-binding transcription factors. Nature. 1995 Jan 26;373(6512):360–362. doi: 10.1038/373360a0. [DOI] [PubMed] [Google Scholar]
  14. Herr W., Sturm R. A., Clerc R. G., Corcoran L. M., Baltimore D., Sharp P. A., Ingraham H. A., Rosenfeld M. G., Finney M., Ruvkun G. 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. 1988 Dec;2(12A):1513–1516. doi: 10.1101/gad.2.12a.1513. [DOI] [PubMed] [Google Scholar]
  15. Hill C. S., Wynne J., Treisman R. Serum-regulated transcription by serum response factor (SRF): a novel role for the DNA binding domain. EMBO J. 1994 Nov 15;13(22):5421–5432. doi: 10.1002/j.1460-2075.1994.tb06877.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Katan M., Haigh A., Verrijzer C. P., van der Vliet P. C., O'Hare P. Characterization of a cellular factor which interacts functionally with Oct-1 in the assembly of a multicomponent transcription complex. Nucleic Acids Res. 1990 Dec 11;18(23):6871–6880. doi: 10.1093/nar/18.23.6871. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Kaushansky K., Shoemaker S. G., O'Rork C. A., McCarty J. M. Coordinate regulation of multiple human lymphokine genes by Oct-1 and potentially novel 45 and 43 kDa polypeptides. J Immunol. 1994 Feb 15;152(4):1812–1820. [PubMed] [Google Scholar]
  18. Kristie T. M., LeBowitz J. H., Sharp P. A. The octamer-binding proteins form multi-protein--DNA complexes with the HSV alpha TIF regulatory protein. EMBO J. 1989 Dec 20;8(13):4229–4238. doi: 10.1002/j.1460-2075.1989.tb08608.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Kristie T. M., Roizman B. Host cell proteins bind to the cis-acting site required for virion-mediated induction of herpes simplex virus 1 alpha genes. Proc Natl Acad Sci U S A. 1987 Jan;84(1):71–75. doi: 10.1073/pnas.84.1.71. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. LaBella F., Sive H. L., Roeder R. G., Heintz N. Cell-cycle regulation of a human histone H2b gene is mediated by the H2b subtype-specific consensus element. Genes Dev. 1988 Jan;2(1):32–39. doi: 10.1101/gad.2.1.32. [DOI] [PubMed] [Google Scholar]
  21. Lefstin J. A., Thomas J. R., Yamamoto K. R. Influence of a steroid receptor DNA-binding domain on transcriptional regulatory functions. Genes Dev. 1994 Dec 1;8(23):2842–2856. doi: 10.1101/gad.8.23.2842. [DOI] [PubMed] [Google Scholar]
  22. Lewis J. B., Thompson Y. G., Caughman G. B. Transcriptional control of the equine herpesvirus 1 immediate early gene. Virology. 1993 Dec;197(2):788–792. doi: 10.1006/viro.1993.1658. [DOI] [PubMed] [Google Scholar]
  23. Luo Y., Roeder R. G. Cloning, functional characterization, and mechanism of action of the B-cell-specific transcriptional coactivator OCA-B. Mol Cell Biol. 1995 Aug;15(8):4115–4124. doi: 10.1128/mcb.15.8.4115. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Marsden H. S., Campbell M. E., Haarr L., Frame M. C., Parris D. S., Murphy M., Hope R. G., Muller M. T., Preston C. M. The 65,000-Mr DNA-binding and virion trans-inducing proteins of herpes simplex virus type 1. J Virol. 1987 Aug;61(8):2428–2437. doi: 10.1128/jvi.61.8.2428-2437.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Mason J. O., Williams G. T., Neuberger M. S. Transcription cell type specificity is conferred by an immunoglobulin VH gene promoter that includes a functional consensus sequence. Cell. 1985 Jun;41(2):479–487. doi: 10.1016/s0092-8674(85)80021-0. [DOI] [PubMed] [Google Scholar]
  26. McKee T. A., Disney G. H., Everett R. D., Preston C. M. Control of expression of the varicella-zoster virus major immediate early gene. J Gen Virol. 1990 Apr;71(Pt 4):897–906. doi: 10.1099/0022-1317-71-4-897. [DOI] [PubMed] [Google Scholar]
  27. McKnight J. L., Kristie T. M., Roizman B. Binding of the virion protein mediating alpha gene induction in herpes simplex virus 1-infected cells to its cis site requires cellular proteins. Proc Natl Acad Sci U S A. 1987 Oct;84(20):7061–7065. doi: 10.1073/pnas.84.20.7061. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Meyer K. B., Neuberger M. S. The immunoglobulin kappa locus contains a second, stronger B-cell-specific enhancer which is located downstream of the constant region. EMBO J. 1989 Jul;8(7):1959–1964. doi: 10.1002/j.1460-2075.1989.tb03601.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Misra V., Bratanich A. C., Carpenter D., O'Hare P. Protein and DNA elements involved in transactivation of the promoter of the bovine herpesvirus (BHV) 1 IE-1 transcription unit by the BHV alpha gene trans-inducing factor. J Virol. 1994 Aug;68(8):4898–4909. doi: 10.1128/jvi.68.8.4898-4909.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Misra V., Walker S., Hayes S., O'Hare P. The bovine herpesvirus alpha gene trans-inducing factor activates transcription by mechanisms different from those of its herpes simplex virus type 1 counterpart VP16. J Virol. 1995 Sep;69(9):5209–5216. doi: 10.1128/jvi.69.9.5209-5216.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Mizushima-Sugano J., Roeder R. G. Cell-type-specific transcription of an immunoglobulin kappa light chain gene in vitro. Proc Natl Acad Sci U S A. 1986 Nov;83(22):8511–8515. doi: 10.1073/pnas.83.22.8511. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. O'Hare P., Goding C. R., Haigh A. 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. 1988 Dec 20;7(13):4231–4238. doi: 10.1002/j.1460-2075.1988.tb03320.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. O'Hare P., Goding C. R. Herpes simplex virus regulatory elements and the immunoglobulin octamer domain bind a common factor and are both targets for virion transactivation. Cell. 1988 Feb 12;52(3):435–445. doi: 10.1016/s0092-8674(88)80036-9. [DOI] [PubMed] [Google Scholar]
  34. O'Rourke D., O'Hare P. Mutually exclusive binding of two cellular factors within a critical promoter region of the gene for the IE110k protein of herpes simplex virus. J Virol. 1993 Dec;67(12):7201–7214. doi: 10.1128/jvi.67.12.7201-7214.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Preston C. M., Frame M. C., Campbell M. E. A complex formed between cell components and an HSV structural polypeptide binds to a viral immediate early gene regulatory DNA sequence. Cell. 1988 Feb 12;52(3):425–434. doi: 10.1016/s0092-8674(88)80035-7. [DOI] [PubMed] [Google Scholar]
  36. Purewal A. S., Allsopp R., Riggio M., Telford E. A., Azam S., Davison A. J., Edington N. Equid herpesviruses 1 and 4 encode functional homologs of the herpes simplex virus type 1 virion transactivator protein, VP16. Virology. 1994 Jan;198(1):385–389. doi: 10.1006/viro.1994.1047. [DOI] [PubMed] [Google Scholar]
  37. Purewal A. S., Smallwood A. V., Kaushal A., Adegboye D., Edington N. Identification and control of the cis-acting elements of the immediate early gene of equid herpesvirus type 1. J Gen Virol. 1992 Mar;73(Pt 3):513–519. doi: 10.1099/0022-1317-73-3-513. [DOI] [PubMed] [Google Scholar]
  38. Ruvkun G., Finney M. Regulation of transcription and cell identity by POU domain proteins. Cell. 1991 Feb 8;64(3):475–478. doi: 10.1016/0092-8674(91)90227-p. [DOI] [PubMed] [Google Scholar]
  39. Schier A. F., Gehring W. J. Functional specificity of the homeodomain protein fushi tarazu: the role of DNA-binding specificity in vivo. Proc Natl Acad Sci U S A. 1993 Feb 15;90(4):1450–1454. doi: 10.1073/pnas.90.4.1450. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Stern S., Tanaka M., Herr W. The Oct-1 homoeodomain directs formation of a multiprotein-DNA complex with the HSV transactivator VP16. Nature. 1989 Oct 19;341(6243):624–630. doi: 10.1038/341624a0. [DOI] [PubMed] [Google Scholar]
  41. Strubin M., Newell J. W., Matthias P. OBF-1, a novel B cell-specific coactivator that stimulates immunoglobulin promoter activity through association with octamer-binding proteins. Cell. 1995 Feb 10;80(3):497–506. doi: 10.1016/0092-8674(95)90500-6. [DOI] [PubMed] [Google Scholar]
  42. Tullius T. D., Dombroski B. A., Churchill M. E., Kam L. Hydroxyl radical footprinting: a high-resolution method for mapping protein-DNA contacts. Methods Enzymol. 1987;155:537–558. doi: 10.1016/0076-6879(87)55035-2. [DOI] [PubMed] [Google Scholar]
  43. Tullius T. D. Physical studies of protein-DNA complexes by footprinting. Annu Rev Biophys Biophys Chem. 1989;18:213–237. doi: 10.1146/annurev.bb.18.060189.001241. [DOI] [PubMed] [Google Scholar]
  44. Ullman K. S., Flanagan W. M., Edwards C. A., Crabtree G. R. Activation of early gene expression in T lymphocytes by Oct-1 and an inducible protein, OAP40. Science. 1991 Oct 25;254(5031):558–562. doi: 10.1126/science.1683003. [DOI] [PubMed] [Google Scholar]
  45. Verrijzer C. P., Van der Vliet P. C. POU domain transcription factors. Biochim Biophys Acta. 1993 Apr 29;1173(1):1–21. doi: 10.1016/0167-4781(93)90237-8. [DOI] [PubMed] [Google Scholar]
  46. Walker S., Hayes S., O'Hare P. Site-specific conformational alteration of the Oct-1 POU domain-DNA complex as the basis for differential recognition by Vmw65 (VP16). Cell. 1994 Dec 2;79(5):841–852. doi: 10.1016/0092-8674(94)90073-6. [DOI] [PubMed] [Google Scholar]
  47. Wegner M., Drolet D. W., Rosenfeld M. G. POU-domain proteins: structure and function of developmental regulators. Curr Opin Cell Biol. 1993 Jun;5(3):488–498. doi: 10.1016/0955-0674(93)90015-i. [DOI] [PubMed] [Google Scholar]
  48. Wilson A. C., LaMarco K., Peterson M. G., Herr W. The VP16 accessory protein HCF is a family of polypeptides processed from a large precursor protein. Cell. 1993 Jul 16;74(1):115–125. doi: 10.1016/0092-8674(93)90299-6. [DOI] [PubMed] [Google Scholar]
  49. Wu C. Two protein-binding sites in chromatin implicated in the activation of heat-shock genes. Nature. 1984 May 17;309(5965):229–234. doi: 10.1038/309229a0. [DOI] [PubMed] [Google Scholar]
  50. Xiao P., Capone J. P. A cellular factor binds to the herpes simplex virus type 1 transactivator Vmw65 and is required for Vmw65-dependent protein-DNA complex assembly with Oct-1. Mol Cell Biol. 1990 Sep;10(9):4974–4977. doi: 10.1128/mcb.10.9.4974. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Zhou D. X., Yen T. S. The ubiquitous transcription factor Oct-1 and the liver-specific factor HNF-1 are both required to activate transcription of a hepatitis B virus promoter. Mol Cell Biol. 1991 Mar;11(3):1353–1359. doi: 10.1128/mcb.11.3.1353. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. apRhys C. M., Ciufo D. M., O'Neill E. A., Kelly T. J., Hayward G. S. Overlapping octamer and TAATGARAT motifs in the VF65-response elements in herpes simplex virus immediate-early promoters represent independent binding sites for cellular nuclear factor III. J Virol. 1989 Jun;63(6):2798–2812. doi: 10.1128/jvi.63.6.2798-2812.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]

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