Skip to main content
NCBI home page
Molecular and Cellular Biology logoLink to Molecular and Cellular Biology
. 1989 Sep;9(9):3821–3828. doi: 10.1128/mcb.9.9.3821

Identification of HeLa cell nuclear factors that bind to and activate the early promoter of human polyomavirus BK in vitro.

T Chakraborty 1, G C Das 1
PMCID: PMC362443  PMID: 2550803

Abstract

Human polyomavirus BK (BKV), an oncogenic DNA virus, differs from other papovaviruses in the organization of the regulatory region and in tissue tropism for kidney cells. The noncoding regulatory region of the viral genome in prototype strains includes three 68-base-pair (bp) repeats, each containing a number of potential regulatory elements. Some of these signals are unique to human papovaviruses, and others are homologous to those identified in many viral and cellular genes. We evaluated the contribution of individual 68-bp repeats to the initiation of transcription from the early promoter in a HeLa cell extract and identified cis-acting elements to which human cellular factors bind to activate transcription. The early promoter with only one copy of the 68-bp repeat could accurately initiate transcription in vitro, but additional copies were required for its stimulation. DNA-binding assays and DNase I protection experiments identified six domains in the regulatory region protected by human cellular factors. Two of these footprints were located within the proximal and distal 68-bp repeats, and one was located at the late side of the repeats. These footprints were centered over a TGGA(N)5-6GCCA core and were produced by a protein of the nuclear factor 1 (NF-1) family. This protein is either identical or similar to that which binds to the high-affinity site at the origin of adenovirus DNA replication. Three other domains, two at the junctions of the 68-bp repeats and one in the late side of the repeats, were partially protected by proteins with AP-1- and Sp-1-like activities. Transcription initiation from the early promoter was drastically reduced when a complete 68-bp repeat or the NF-1 binding site was used as a competitor in the in vitro assay. However, a point mutation within the NF-1 binding site, which reduced NF-1 binding in vitro to a level comparable to that of nonspecific DNA, also eliminated its ability to compete with early transcription. The murine homolog of the AP-1 binding site had a modest effect on in vitro transcription. Our results suggest that, among the multiple HeLa cell nuclear factors, NF-1 acts as a major activator of the early promoter in vitro.

Full text

PDF
3821

Images in this article

3823Image
on p.3823
3823Image
on p.3823
3824Image
on p.3824
3825Image
on p.3825
3826Image
on p.3826
3826Image
on p.3826

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Arthur R. R., Shah K. V., Baust S. J., Santos G. W., Saral R. Association of BK viruria with hemorrhagic cystitis in recipients of bone marrow transplants. N Engl J Med. 1986 Jul 24;315(4):230–234. doi: 10.1056/NEJM198607243150405. [DOI] [PubMed] [Google Scholar]
  2. Arthur R. R., Shah K. V., Charache P., Saral R. BK and JC virus infections in recipients of bone marrow transplants. J Infect Dis. 1988 Sep;158(3):563–569. doi: 10.1093/infdis/158.3.563. [DOI] [PubMed] [Google Scholar]
  3. Berg D. T., Walls J. D., Grinnell B. W. A variant enhancer/regulatory region from a cloned human prototype BK virus genome. Nucleic Acids Res. 1988 Sep 26;16(18):9057–9057. doi: 10.1093/nar/16.18.9057. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Briggs M. R., Kadonaga J. T., Bell S. P., Tjian R. Purification and biochemical characterization of the promoter-specific transcription factor, Sp1. Science. 1986 Oct 3;234(4772):47–52. doi: 10.1126/science.3529394. [DOI] [PubMed] [Google Scholar]
  5. Caputo A., Corallini A., Grossi M. P., Carrà L., Balboni P. G., Negrini M., Milanesi G., Federspil G., Barbanti-Brodano G. Episomal DNA of a BK virus variant in a human insulinoma. J Med Virol. 1983;12(1):37–49. doi: 10.1002/jmv.1890120105. [DOI] [PubMed] [Google Scholar]
  6. Chauhan S., Lecatsas G., Harley E. H. Genome analysis of BK (WW) viral DNA cloned directly from human urine. Intervirology. 1984;22(3):170–176. doi: 10.1159/000149547. [DOI] [PubMed] [Google Scholar]
  7. Chodosh L. A., Baldwin A. S., Carthew R. W., Sharp P. A. Human CCAAT-binding proteins have heterologous subunits. Cell. 1988 Apr 8;53(1):11–24. doi: 10.1016/0092-8674(88)90483-7. [DOI] [PubMed] [Google Scholar]
  8. Das G. C., Piatigorsky J. The chicken delta 1-crystallin gene promoter: binding of transcription factor(s) to the upstream G+C-rich region is necessary for promoter function in vitro. Proc Natl Acad Sci U S A. 1986 May;83(10):3131–3135. doi: 10.1073/pnas.83.10.3131. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Das G. C., Salzman N. P. Simian virus 40 early promoter mutations that affect promoter function and autoregulation by large T antigen. J Mol Biol. 1985 Mar 20;182(2):229–239. doi: 10.1016/0022-2836(85)90341-9. [DOI] [PubMed] [Google Scholar]
  10. Deyerle K. L., Cassill J. A., Subramani S. Analysis of the early regulatory region of the human papovavirus BK. Virology. 1987 May;158(1):181–193. doi: 10.1016/0042-6822(87)90252-2. [DOI] [PubMed] [Google Scholar]
  11. Deyerle K. L., Subramani S. Linker scan analysis of the early regulatory region of human papovavirus BK. J Virol. 1988 Sep;62(9):3378–3387. doi: 10.1128/jvi.62.9.3378-3387.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Dignam J. D., Lebovitz R. M., Roeder R. G. Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. Nucleic Acids Res. 1983 Mar 11;11(5):1475–1489. doi: 10.1093/nar/11.5.1475. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Dorn A., Bollekens J., Staub A., Benoist C., Mathis D. A multiplicity of CCAAT box-binding proteins. Cell. 1987 Sep 11;50(6):863–872. doi: 10.1016/0092-8674(87)90513-7. [DOI] [PubMed] [Google Scholar]
  14. Dynan W. S., Tjian R. The promoter-specific transcription factor Sp1 binds to upstream sequences in the SV40 early promoter. Cell. 1983 Nov;35(1):79–87. doi: 10.1016/0092-8674(83)90210-6. [DOI] [PubMed] [Google Scholar]
  15. Gardner S. D., Field A. M., Coleman D. V., Hulme B. New human papovavirus (B.K.) isolated from urine after renal transplantation. Lancet. 1971 Jun 19;1(7712):1253–1257. doi: 10.1016/s0140-6736(71)91776-4. [DOI] [PubMed] [Google Scholar]
  16. Garner M. M., Revzin A. A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions: application to components of the Escherichia coli lactose operon regulatory system. Nucleic Acids Res. 1981 Jul 10;9(13):3047–3060. doi: 10.1093/nar/9.13.3047. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Grinnell B. W., Berg D. T., Walls J. D. Negative regulation of the human polyomavirus BK enhancer involves cell-specific interaction with a nuclear repressor. Mol Cell Biol. 1988 Aug;8(8):3448–3457. doi: 10.1128/mcb.8.8.3448. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Gronostajski R. M., Adhya S., Nagata K., Guggenheimer R. A., Hurwitz J. Site-specific DNA binding of nuclear factor I: analyses of cellular binding sites. Mol Cell Biol. 1985 May;5(5):964–971. doi: 10.1128/mcb.5.5.964. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Gronostajski R. M., Knox J., Berry D., Miyamoto N. G. Stimulation of transcription in vitro by binding sites for nuclear factor I. Nucleic Acids Res. 1988 Mar 25;16(5):2087–2098. doi: 10.1093/nar/16.5.2087. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Hara K., Oya Y., Yogo Y. Enhancement of the transforming capacity of BK virus by partial deletion of the 68-base-pair tandem repeats. J Virol. 1985 Sep;55(3):867–869. doi: 10.1128/jvi.55.3.867-869.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Jackson S. P., Tjian R. O-glycosylation of eukaryotic transcription factors: implications for mechanisms of transcriptional regulation. Cell. 1988 Oct 7;55(1):125–133. doi: 10.1016/0092-8674(88)90015-3. [DOI] [PubMed] [Google Scholar]
  22. Jeang K. T., Rawlins D. R., Rosenfeld P. J., Shero J. H., Kelly T. J., Hayward G. S. Multiple tandemly repeated binding sites for cellular nuclear factor 1 that surround the major immediate-early promoters of simian and human cytomegalovirus. J Virol. 1987 May;61(5):1559–1570. doi: 10.1128/jvi.61.5.1559-1570.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Jones K. A., Kadonaga J. T., Rosenfeld P. J., Kelly T. J., Tjian R. A cellular DNA-binding protein that activates eukaryotic transcription and DNA replication. Cell. 1987 Jan 16;48(1):79–89. doi: 10.1016/0092-8674(87)90358-8. [DOI] [PubMed] [Google Scholar]
  24. Jones K. A., Luciw P. A., Duchange N. Structural arrangements of transcription control domains within the 5'-untranslated leader regions of the HIV-1 and HIV-2 promoters. Genes Dev. 1988 Sep;2(9):1101–1114. doi: 10.1101/gad.2.9.1101. [DOI] [PubMed] [Google Scholar]
  25. Jones K. A., Yamamoto K. R., Tjian R. Two distinct transcription factors bind to the HSV thymidine kinase promoter in vitro. Cell. 1985 Sep;42(2):559–572. doi: 10.1016/0092-8674(85)90113-8. [DOI] [PubMed] [Google Scholar]
  26. Knight G. B., Gudas J. M., Pardee A. B. Cell-cycle-specific interaction of nuclear DNA-binding proteins with a CCAAT sequence from the human thymidine kinase gene. Proc Natl Acad Sci U S A. 1987 Dec;84(23):8350–8354. doi: 10.1073/pnas.84.23.8350. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Lee W., Mitchell P., Tjian R. Purified transcription factor AP-1 interacts with TPA-inducible enhancer elements. Cell. 1987 Jun 19;49(6):741–752. doi: 10.1016/0092-8674(87)90612-x. [DOI] [PubMed] [Google Scholar]
  28. Manley J. L., Fire A., Cano A., Sharp P. A., Gefter M. L. DNA-dependent transcription of adenovirus genes in a soluble whole-cell extract. Proc Natl Acad Sci U S A. 1980 Jul;77(7):3855–3859. doi: 10.1073/pnas.77.7.3855. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Markowitz R. B., Dynan W. S. Binding of cellular proteins to the regulatory region of BK virus DNA. J Virol. 1988 Sep;62(9):3388–3398. doi: 10.1128/jvi.62.9.3388-3398.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
  31. Nagata K., Guggenheimer R. A., Hurwitz J. Specific binding of a cellular DNA replication protein to the origin of replication of adenovirus DNA. Proc Natl Acad Sci U S A. 1983 Oct;80(20):6177–6181. doi: 10.1073/pnas.80.20.6177. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Nowock J., Borgmeyer U., Püschel A. W., Rupp R. A., Sippel A. E. The TGGCA protein binds to the MMTV-LTR, the adenovirus origin of replication, and the BK virus enhancer. Nucleic Acids Res. 1985 Mar 25;13(6):2045–2061. doi: 10.1093/nar/13.6.2045. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Pagnani M., Negrini M., Reschiglian P., Corallini A., Balboni P. G., Scherneck S., Macino G., Milanesi G., Barbanti-Brodano G. Molecular and biological properties of BK virus-IR, a BK virus variant isolated from a human tumor. J Virol. 1986 Aug;59(2):500–505. doi: 10.1128/jvi.59.2.500-505.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Pater A., Pater M. M., Chang L. S., Slawin K., Di Mayorca G. Multiple origins of the complementary defective genomes of RF and origin proximal sequences of GS, two human papovavirus isolates. Virology. 1983 Dec;131(2):426–436. doi: 10.1016/0042-6822(83)90509-3. [DOI] [PubMed] [Google Scholar]
  35. Rosenfeld P. J., Kelly T. J. Purification of nuclear factor I by DNA recognition site affinity chromatography. J Biol Chem. 1986 Jan 25;261(3):1398–1408. [PubMed] [Google Scholar]
  36. Rosenfeld P. J., O'Neill E. A., Wides R. J., Kelly T. J. Sequence-specific interactions between cellular DNA-binding proteins and the adenovirus origin of DNA replication. Mol Cell Biol. 1987 Feb;7(2):875–886. doi: 10.1128/mcb.7.2.875. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Rosenthal N., Kress M., Gruss P., Khoury G. BK viral enhancer element and a human cellular homolog. Science. 1983 Nov 18;222(4625):749–755. doi: 10.1126/science.6314501. [DOI] [PubMed] [Google Scholar]
  38. Rubinstein R., Pare N., Harley E. H. Structure and function of the transcriptional control region of nonpassaged BK virus. J Virol. 1987 May;61(5):1747–1750. doi: 10.1128/jvi.61.5.1747-1750.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Santoro C., Mermod N., Andrews P. C., Tjian R. A family of human CCAAT-box-binding proteins active in transcription and DNA replication: cloning and expression of multiple cDNAs. Nature. 1988 Jul 21;334(6179):218–224. doi: 10.1038/334218a0. [DOI] [PubMed] [Google Scholar]
  40. Sawadogo M., Roeder R. G. Factors involved in specific transcription by human RNA polymerase II: analysis by a rapid and quantitative in vitro assay. Proc Natl Acad Sci U S A. 1985 Jul;82(13):4394–4398. doi: 10.1073/pnas.82.13.4394. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Schaffner G., Schirm S., Müller-Baden B., Weber F., Schaffner W. Redundancy of information in enhancers as a principle of mammalian transcription control. J Mol Biol. 1988 May 5;201(1):81–90. doi: 10.1016/0022-2836(88)90440-8. [DOI] [PubMed] [Google Scholar]
  42. Schorpp M., Kugler W., Wagner U., Ryffel G. U. Hepatocyte-specific promoter element HP1 of the Xenopus albumin gene interacts with transcriptional factors of mammalian hepatocytes. J Mol Biol. 1988 Jul 20;202(2):307–320. doi: 10.1016/0022-2836(88)90460-3. [DOI] [PubMed] [Google Scholar]
  43. Seif I., Khoury G., Dhar R. The genome of human papovavirus BKV. Cell. 1979 Dec;18(4):963–977. doi: 10.1016/0092-8674(79)90209-5. [DOI] [PubMed] [Google Scholar]
  44. Small J. A., Khoury G., Jay G., Howley P. M., Scangos G. A. Early regions of JC virus and BK virus induce distinct and tissue-specific tumors in transgenic mice. Proc Natl Acad Sci U S A. 1986 Nov;83(21):8288–8292. doi: 10.1073/pnas.83.21.8288. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Tamura T., Miura M., Ikenaka K., Mikoshiba K. Analysis of transcription control elements of the mouse myelin basic protein gene in HeLa cell extracts: demonstration of a strong NFI-binding motif in the upstream region. Nucleic Acids Res. 1988 Dec 23;16(24):11441–11459. doi: 10.1093/nar/16.24.11441. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Uchida S., Watanabe S., Aizawa T., Furuno A., Muto T. Polyoncogenicity and insulinoma-inducing ability of BK Virus, a human Papovavirus, in Syrian golden hamsters. J Natl Cancer Inst. 1979 Jul;63(1):119–126. [PubMed] [Google Scholar]
  47. Watanabe S., Yoshiike K. Change of DNA near the origin of replication enhances the transforming capacity of human papovavirus BK. J Virol. 1982 Jun;42(3):978–985. doi: 10.1128/jvi.42.3.978-985.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Watanabe S., Yoshiike K. Decreasing the number of 68-base-pair tandem repeats in the BK virus transcriptional control region reduces plaque size and enhances transforming capacity. J Virol. 1985 Sep;55(3):823–825. doi: 10.1128/jvi.55.3.823-825.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Yang R. C., Wu R. BK virus DNA: complete nucleotide sequence of a human tumor virus. Science. 1979 Oct 26;206(4417):456–462. doi: 10.1126/science.228391. [DOI] [PubMed] [Google Scholar]
  50. de Ronde A., MacDonald M., Sol C., ter Schegget J., Wouters E., van Strien A., van der Noordaa J. The early enhancer-promoter of BKV and host range for transformation. Intervirology. 1987;27(1):38–44. doi: 10.1159/000149713. [DOI] [PubMed] [Google Scholar]
  51. de Vries E., van Driel W., van den Heuvel S. J., van der Vliet P. C. Contactpoint analysis of the HeLa nuclear factor I recognition site reveals symmetrical binding at one side of the DNA helix. EMBO J. 1987 Jan;6(1):161–168. doi: 10.1002/j.1460-2075.1987.tb04734.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. ter Schegget J., Sol C. J., Baan E. W., van der Noordaa J., van Ormondt H. Naturally occurring BK virus variants (JL and Dik) with deletions in the putative early enhancer-promoter sequences. J Virol. 1985 Jan;53(1):302–305. doi: 10.1128/jvi.53.1.302-305.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Molecular and Cellular Biology are provided here courtesy of Taylor & Francis

RESOURCES