Skip to main content
NCBI home page
Journal of Virology logoLink to Journal of Virology
. 1986 Feb;57(2):505–514. doi: 10.1128/jvi.57.2.505-514.1986

Guanine nucleotide contacts within viral DNA sequences bound by polyomavirus large T antigen.

A Cowie, R Kamen
PMCID: PMC252763  PMID: 3003383

Abstract

Essential nucleotide contacts between the polyomavirus large T antigen and its multiple specific binding regions within the regulatory sequences of the polyomavirus genome were determined in vitro by methylation interference. Methylation of any of the guanine residues of the 5'-G(A/G)GGC-3' pentanucleotide repeats in large-T-antigen-binding regions A, B, C, and 3 (A. Cowie and R. Kamen, J. Virol. 52:750-760, 1984) interfered with T antigen binding. Within regions A, B, and C these pentanucleotides are spaced 5 or 6 base pairs apart. Therefore, the clusters of contacted nucleotides within each of these binding regions are localized along one face of the DNA helix. Methylation of guanines within the sequences between the pentanucleotide repeats did not interfere with binding. The ORI binding region contains four additional pentanucleotide sequences within a region of dyad symmetry. Methylation of only particular guanines of these pentanucleotides interfered with T antigen binding. The spatial arrangement of the pentanucleotides in the ORI is such that the clusters of contacted guanines are situated around the DNA helix, thereby forming a very different arrangement from that found in the other binding regions. A model is discussed in which cooperative interactions between T antigen protomers, recognizing individual pentanucleotides, determines the strength and the function of different T antigen-DNA interactions.

Full text

PDF
505

Images in this article

507Image
on p.507
507Image
on p.507
508Image
on p.508
509Image
on p.509
510Image
on p.510
510Image
on p.510
511Image
on p.511

Selected References

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

  1. Bradley M. K., Hudson J., Villanueva M. S., Livingston D. M. Specific in vitro adenylylation of the simian virus 40 large tumor antigen. Proc Natl Acad Sci U S A. 1984 Nov;81(21):6574–6578. doi: 10.1073/pnas.81.21.6574. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Brady J., Bolen J. B., Radonovich M., Salzman N., Khoury G. Stimulation of simian virus 40 late gene expression by simian virus 40 tumor antigen. Proc Natl Acad Sci U S A. 1984 Apr;81(7):2040–2044. doi: 10.1073/pnas.81.7.2040. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Clayton C. E., Murphy D., Lovett M., Rigby P. W. A fragment of the SV40 large T-antigen gene transforms. Nature. 1982 Sep 2;299(5878):59–61. doi: 10.1038/299059a0. [DOI] [PubMed] [Google Scholar]
  4. Clertant P., Gaudray P., May E., Cuzin F. The nucleotide binding site detected by affinity labeling in the large T proteins of polyoma and SV40 viruses is distinct from their ATPase catalytic site. J Biol Chem. 1984 Dec 25;259(24):15196–15203. [PubMed] [Google Scholar]
  5. Colby W. W., Chen E. Y., Smith D. H., Levinson A. D. Identification and nucleotide sequence of a human locus homologous to the v-myc oncogene of avian myelocytomatosis virus MC29. Nature. 1983 Feb 24;301(5902):722–725. doi: 10.1038/301722a0. [DOI] [PubMed] [Google Scholar]
  6. Cowie A., Jat P., Kamen R. Determination of sequences at the capped 5' ends of polyoma virus early region transcripts synthesized in vivo and in vitro demonstrates an unusual microheterogeneity. J Mol Biol. 1982 Aug 5;159(2):225–255. doi: 10.1016/0022-2836(82)90494-6. [DOI] [PubMed] [Google Scholar]
  7. Cowie A., Kamen R. Multiple binding sites for polyomavirus large T antigen within regulatory sequences of polyomavirus DNA. J Virol. 1984 Dec;52(3):750–760. doi: 10.1128/jvi.52.3.750-760.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. DeLucia A. L., Lewton B. A., Tjian R., Tegtmeyer P. Topography of simian virus 40 A protein-DNA complexes: arrangement of pentanucleotide interaction sites at the origin of replication. J Virol. 1983 Apr;46(1):143–150. doi: 10.1128/jvi.46.1.143-150.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Dilworth S. M., Cowie A., Kamen R. I., Griffin B. E. DNA binding activity of polyoma virus large tumor antigen. Proc Natl Acad Sci U S A. 1984 Apr;81(7):1941–1945. doi: 10.1073/pnas.81.7.1941. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. 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]
  11. Hunt C., Morimoto R. I. Conserved features of eukaryotic hsp70 genes revealed by comparison with the nucleotide sequence of human hsp70. Proc Natl Acad Sci U S A. 1985 Oct;82(19):6455–6459. doi: 10.1073/pnas.82.19.6455. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Jat P., Novak U., Cowie A., Tyndall C., Kamen R. DNA sequences required for specific and efficient initiation of transcription at the polyoma virus early promoter. Mol Cell Biol. 1982 Jul;2(7):737–751. doi: 10.1128/mcb.2.7.737. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Jones K. A., Tjian R. Essential contact residues within SV40 large T antigen binding sites I and II identified by alkylation-interference. Cell. 1984 Jan;36(1):155–162. doi: 10.1016/0092-8674(84)90084-9. [DOI] [PubMed] [Google Scholar]
  14. Kalderon D., Oostra B. A., Ely B. K., Smith A. E. Deletion loop mutagenesis: a novel method for the construction of point mutations using deletion mutants. Nucleic Acids Res. 1982 Sep 11;10(17):5161–5171. doi: 10.1093/nar/10.17.5161. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Kamen R., Jat P., Treisman R., Favaloro J., Folk W. R. 5' termini of polyoma virus early region transcripts synthesized in vivo by wild-type virus and viable deletion mutants. J Mol Biol. 1982 Aug 5;159(2):189–224. doi: 10.1016/0022-2836(82)90493-4. [DOI] [PubMed] [Google Scholar]
  16. Katinka M., Yaniv M. DNA replication origin of polyoma virus: early proximal boundary. J Virol. 1983 Jul;47(1):244–248. doi: 10.1128/jvi.47.1.244-248.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Keller J. M., Alwine J. C. Activation of the SV40 late promoter: direct effects of T antigen in the absence of viral DNA replication. Cell. 1984 Feb;36(2):381–389. doi: 10.1016/0092-8674(84)90231-9. [DOI] [PubMed] [Google Scholar]
  18. Land H., Parada L. F., Weinberg R. A. Tumorigenic conversion of primary embryo fibroblasts requires at least two cooperating oncogenes. Nature. 1983 Aug 18;304(5927):596–602. doi: 10.1038/304596a0. [DOI] [PubMed] [Google Scholar]
  19. Luthman H., Nilsson M. G., Magnusson G. Non-contiguous segments of the polyoma genome required in cis for DNA replication. J Mol Biol. 1982 Nov 15;161(4):533–550. doi: 10.1016/0022-2836(82)90406-5. [DOI] [PubMed] [Google Scholar]
  20. Luthman H., Osterlund M., Magnusson G. Inhibition of polyoma DNA synthesis by base pair substitutions at the replication origin. Nucleic Acids Res. 1984 Oct 11;12(19):7503–7515. doi: 10.1093/nar/12.19.7503. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. 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]
  22. McGrogan M., Simonsen C. C., Smouse D. T., Farnham P. J., Schimke R. T. Heterogeneity at the 5' termini of mouse dihydrofolate reductase mRNAs. Evidence for multiple promoter regions. J Biol Chem. 1985 Feb 25;260(4):2307–2314. [PubMed] [Google Scholar]
  23. McKay R. D. Binding of a simian virus 40 T antigen-related protein to DNA. J Mol Biol. 1981 Jan 25;145(3):471–488. doi: 10.1016/0022-2836(81)90540-4. [DOI] [PubMed] [Google Scholar]
  24. Morrison B., Kress M., Khoury G., Jay G. Simian virus 40 tumor antigen: isolation of the origin-specific DNA-binding domain. J Virol. 1983 Jul;47(1):106–114. doi: 10.1128/jvi.47.1.106-114.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Nilsson S. V., Magnusson G. Activities of polyomavirus large-T-antigen proteins expressed by mutant genes. J Virol. 1984 Sep;51(3):768–775. doi: 10.1128/jvi.51.3.768-775.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Pomerantz B. J., Hassell J. A. Polyomavirus and simian virus 40 large T antigens bind to common DNA sequences. J Virol. 1984 Mar;49(3):925–937. doi: 10.1128/jvi.49.3.925-937.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Pomerantz B. J., Mueller C. R., Hassell J. A. Polyomavirus large T antigen binds independently to multiple, unique regions on the viral genome. J Virol. 1983 Sep;47(3):600–610. doi: 10.1128/jvi.47.3.600-610.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Rassoulzadegan M., Cowie A., Carr A., Glaichenhaus N., Kamen R., Cuzin F. The roles of individual polyoma virus early proteins in oncogenic transformation. Nature. 1982 Dec 23;300(5894):713–718. doi: 10.1038/300713a0. [DOI] [PubMed] [Google Scholar]
  29. Rassoulzadegan M., Naghashfar Z., Cowie A., Carr A., Grisoni M., Kamen R., Cuzin F. Expression of the large T protein of polyoma virus promotes the establishment in culture of "normal" rodent fibroblast cell lines. Proc Natl Acad Sci U S A. 1983 Jul;80(14):4354–4358. doi: 10.1073/pnas.80.14.4354. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Ruley H. E. Adenovirus early region 1A enables viral and cellular transforming genes to transform primary cells in culture. Nature. 1983 Aug 18;304(5927):602–606. doi: 10.1038/304602a0. [DOI] [PubMed] [Google Scholar]
  31. Schaffhausen B. Transforming genes and gene products of polyoma and SV40. CRC Crit Rev Biochem. 1982;13(3):215–286. doi: 10.3109/10409238209114230. [DOI] [PubMed] [Google Scholar]
  32. Siebenlist U., Gilbert W. Contacts between Escherichia coli RNA polymerase and an early promoter of phage T7. Proc Natl Acad Sci U S A. 1980 Jan;77(1):122–126. doi: 10.1073/pnas.77.1.122. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Tegtmeyer P., Andersen B., Shaw S. B., Wilson V. G. Alternative interactions of the SV40 A protein with DNA. Virology. 1981 Nov;115(1):75–87. doi: 10.1016/0042-6822(81)90090-8. [DOI] [PubMed] [Google Scholar]
  34. Tegtmeyer P., Lewton B. A., DeLucia A. L., Wilson V. G., Ryder K. Topography of simian virus 40 A protein-DNA complexes: arrangement of protein bound to the origin of replication. J Virol. 1983 Apr;46(1):151–161. doi: 10.1128/jvi.46.1.151-161.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Tjian R. Regulation of viral transcription and DNA replication by the SV40 large T antigen. Curr Top Microbiol Immunol. 1981;93:5–24. doi: 10.1007/978-3-642-68123-3_2. [DOI] [PubMed] [Google Scholar]
  36. Triezenberg S. J., Folk W. R. Essential nucleotides in the polyomavirus origin region. J Virol. 1984 Aug;51(2):437–444. doi: 10.1128/jvi.51.2.437-444.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Tyndall C., La Mantia G., Thacker C. M., Favaloro J., Kamen R. A region of the polyoma virus genome between the replication origin and late protein coding sequences is required in cis for both early gene expression and viral DNA replication. Nucleic Acids Res. 1981 Dec 11;9(23):6231–6250. doi: 10.1093/nar/9.23.6231. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Vocke C., Bastia D. DNA-protein interaction at the origin of DNA replication of the plasmid pSC101. Cell. 1983 Dec;35(2 Pt 1):495–502. doi: 10.1016/0092-8674(83)90183-6. [DOI] [PubMed] [Google Scholar]

Articles from Journal of Virology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES