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. 1980 May;34(2):416–430. doi: 10.1128/jvi.34.2.416-430.1980

BK virus DNA sequence coding for the t and T antigens and evaluation of methods for determining sequence homology.

R C Yang, A Young, R Wu
PMCID: PMC288720  PMID: 6246273

Abstract

The DNA sequence of the early region of the human papovavirus BK (MM strain) was determined. A potential initiation signal for translation is located at nucleotides 3,047 to 3,045 or map position 0.614. Extending counterclockwise from this AUG signal there is only one open reading frame, which can code for a putative t antigen of 100 amino acids in length. If the early mRNA of BKV is spliced, then the regions between nucleotides 3,047 to 2,808 and 2,725 to 884 can code for a T antigen 694 amino acids in length. The sequences of the deduced T antigens in BK virus share 71% amino acid homology with those in simian virus 40, whereas the coding sequences of the two viruses share 70% DNA homology. Comparison of DNA sequences and evaluation of homology measurements between these two viruses are discussed.

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Selected References

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

  1. Aloni Y., Dhar R., Laub O., Horowitz M., Khoury G. Novel mechanism for RNA maturation: the leader sequences of simian virus 40 mRNA are not transcribed adjacent to the coding sequences. Proc Natl Acad Sci U S A. 1977 Sep;74(9):3686–3690. doi: 10.1073/pnas.74.9.3686. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Berk A. J., Sharp P. A. Spliced early mRNAs of simian virus 40. Proc Natl Acad Sci U S A. 1978 Mar;75(3):1274–1278. doi: 10.1073/pnas.75.3.1274. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Cole C. N., Landers T., Goff S. P., Manteuil-Brutlag S., Berg P. Physical and genetic characterization of deletion mutants of simian virus 40 constructed in vitro. J Virol. 1977 Oct;24(1):277–294. doi: 10.1128/jvi.24.1.277-294.1977. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Crawford L. V., Cole C. N., Smith A. E., Paucha E., Tegtmeyer P., Rundell K., Berg P. Organization and expression of early genes of simian virus 40. Proc Natl Acad Sci U S A. 1978 Jan;75(1):117–121. doi: 10.1073/pnas.75.1.117. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Dhar R., Lai C. J., Khoury G. Nucleotide sequence of the DNA replication origin for human papovavirus BKV: sequence and structural homology with SV40. Cell. 1978 Feb;13(2):345–358. doi: 10.1016/0092-8674(78)90203-9. [DOI] [PubMed] [Google Scholar]
  6. Dhar R., Seif I., Khoury G. Nucleotide sequence of the BK virus DNA segment encoding small t antigen. Proc Natl Acad Sci U S A. 1979 Feb;76(2):565–569. doi: 10.1073/pnas.76.2.565. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Dodgson J. B., Wells R. D. Synthesis and thermal melting behavior of oligomer-polymer complexes containing defined lengths of mismatched dA-dG and dG-dG nucleotides. Biochemistry. 1977 May 31;16(11):2367–2374. doi: 10.1021/bi00630a009. [DOI] [PubMed] [Google Scholar]
  8. Fareed G. C., Davoli D. Molecular biology of papovaviruses. Annu Rev Biochem. 1977;46:471–522. doi: 10.1146/annurev.bi.46.070177.002351. [DOI] [PubMed] [Google Scholar]
  9. Fiers W., Contreras R., Haegemann G., Rogiers R., Van de Voorde A., Van Heuverswyn H., Van Herreweghe J., Volckaert G., Ysebaert M. Complete nucleotide sequence of SV40 DNA. Nature. 1978 May 11;273(5658):113–120. doi: 10.1038/273113a0. [DOI] [PubMed] [Google Scholar]
  10. Freund J., di Mayorca G., Subramanian K. N. Mapping and ordering of fragments of BK virus DNA produced by restriction endonucleases. J Virol. 1979 Mar;29(3):915–925. doi: 10.1128/jvi.29.3.915-925.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. 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]
  12. Ghosh P. K., Reddy V. B., Swinscoe J., Lebowitz P., Weissman S. M. Heterogeneity and 5'-terminal structures of the late RNAs of simian virus 40. J Mol Biol. 1978 Dec 25;126(4):813–846. doi: 10.1016/0022-2836(78)90022-0. [DOI] [PubMed] [Google Scholar]
  13. Grantham R. Viral, prokaryote and eukaryote genes contrasted by mRNA sequence indexes. FEBS Lett. 1978 Nov 1;95(1):1–11. doi: 10.1016/0014-5793(78)80041-6. [DOI] [PubMed] [Google Scholar]
  14. Hirt B. Selective extraction of polyoma DNA from infected mouse cell cultures. J Mol Biol. 1967 Jun 14;26(2):365–369. doi: 10.1016/0022-2836(67)90307-5. [DOI] [PubMed] [Google Scholar]
  15. Howley P. M., Israel M. A., Law M. F., Martin M. A. A rapid method for detecting and mapping homology between heterologous DNAs. Evaluation of polyomavirus genomes. J Biol Chem. 1979 Jun 10;254(11):4876–4883. [PubMed] [Google Scholar]
  16. Howley P. M., Khoury G., Byrne J. C., Takemoto K. K., Martin M. A. Physical map of the BK virus genome. J Virol. 1975 Oct;16(4):959–973. doi: 10.1128/jvi.16.4.959-973.1975. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Kelly T. J., Jr, Nathans D. The genome of simian virus 40. Adv Virus Res. 1977;21:85–173. doi: 10.1016/s0065-3527(08)60762-9. [DOI] [PubMed] [Google Scholar]
  18. Khoury G., Howley P. M., Garon C., Mullarkey M. F., Takemoto K. K., Martin M. A. Homology and relationship between the genomes of papovaviruses, BK virus and simian virus 40. Proc Natl Acad Sci U S A. 1975 Jul;72(7):2563–2567. doi: 10.1073/pnas.72.7.2563. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Major E. O., Di Mayorca G. Malignant transformation of BHK21 clone 13 cells by BK virus--a human papovavirus. Proc Natl Acad Sci U S A. 1973 Nov;70(11):3210–3212. doi: 10.1073/pnas.70.11.3210. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Martinis J., Croce C. M. Somatic cell hybrids producing antibodies specific for the tumor antigen of simian virus 40. Proc Natl Acad Sci U S A. 1978 May;75(5):2320–2323. doi: 10.1073/pnas.75.5.2320. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Mason D. H., Takemoto K. K. Complementation between BK human papovavirus and a simian virus 40 tsA mutant. J Virol. 1976 Mar;17(3):1060–1062. doi: 10.1128/jvi.17.3.1060-1062.1976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Maxam A. M., Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A. 1977 Feb;74(2):560–564. doi: 10.1073/pnas.74.2.560. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Newell N., Lai C. J., Khoury G., Kelly T. J., Jr Electron microscope study of the base sequence homology between simian virus 40 and human papovavirus BK. J Virol. 1978 Jan;25(1):193–201. doi: 10.1128/jvi.25.1.193-201.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Osborn J. E., Robertson S. M., Padgett B. L., Walker D. L., Weisblum B. Comparison of JC and BK human papovaviruses with simian virus 40: DNA homology studies. J Virol. 1976 Aug;19(2):675–684. doi: 10.1128/jvi.19.2.675-684.1976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Padmanabhan R., Wu R. Nucleotide sequence analysis of DNA. IV. Complete nucleotide sequence of the left-hand cohesive end of coliphage 186 DNA. J Mol Biol. 1972 Apr 14;65(3):447–467. doi: 10.1016/0022-2836(72)90201-x. [DOI] [PubMed] [Google Scholar]
  26. Paucha E., Mellor A., Harvey R., Smith A. E., Hewick R. M., Waterfield M. D. Large and small tumor antigens from simian virus 40 have identical amino termini mapping at 0.65 map units. Proc Natl Acad Sci U S A. 1978 May;75(5):2165–2169. doi: 10.1073/pnas.75.5.2165. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Portolani M., Barbanti-Brodano G., Placa M. L. Malignant transformation of hamster kidney cells by BK virus. J Virol. 1975 Feb;15(2):420–422. doi: 10.1128/jvi.15.2.420-422.1975. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Prives C., Gilboa E., Revel M., Winocour E. Cell-free translation of simian virus 40 early messenger RNA coding for viral T-antigen. Proc Natl Acad Sci U S A. 1977 Feb;74(2):457–461. doi: 10.1073/pnas.74.2.457. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Purchio A. F., Fareed G. C. Transformation of human embryonic kidney cells by human papovarirus BK. J Virol. 1979 Feb;29(2):763–769. doi: 10.1128/jvi.29.2.763-769.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Reddy V. B., Thimmappaya B., Dhar R., Subramanian K. N., Zain B. S., Pan J., Ghosh P. K., Celma M. L., Weissman S. M. The genome of simian virus 40. Science. 1978 May 5;200(4341):494–502. doi: 10.1126/science.205947. [DOI] [PubMed] [Google Scholar]
  31. Sanger F., Coulson A. R. The use of thin acrylamide gels for DNA sequencing. FEBS Lett. 1978 Mar 1;87(1):107–110. doi: 10.1016/0014-5793(78)80145-8. [DOI] [PubMed] [Google Scholar]
  32. 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]
  33. Shah K. V., Daniel R. W., Strandberg J. D. Sarcoma in a hamster inoculated with BK virus, a human papovavirus. J Natl Cancer Inst. 1975 Apr;54(4):945–950. [PubMed] [Google Scholar]
  34. Simmons D. T., Martin M. A. Common methionine-tryptic peptides near the amino-terminal end of primate papovavirus tumor antigens. Proc Natl Acad Sci U S A. 1978 Mar;75(3):1131–1135. doi: 10.1073/pnas.75.3.1131. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Simmons D. T., Takemoto K. K., Martin M. A. Relationship between the methionine tryptic peptides of simian virus 40 and BK virus tumor antigens. J Virol. 1977 Oct;24(1):319–325. doi: 10.1128/jvi.24.1.319-325.1977. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Southern E. M. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol. 1975 Nov 5;98(3):503–517. doi: 10.1016/s0022-2836(75)80083-0. [DOI] [PubMed] [Google Scholar]
  37. Takemoto K. K., Mullarkey M. F. Human papovavirus, BK strain: biological studies including antigenic relationship to simian virus 40. J Virol. 1973 Sep;12(3):625–631. doi: 10.1128/jvi.12.3.625-631.1973. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Takemoto K. K., Rabson A. S., Mullarkey M. F., Blaese R. M., Garon C. F., Nelson D. Isolation of papovavirus from brain tumor and urine of a patient with Wiskott-Aldrich syndrome. J Natl Cancer Inst. 1974 Nov;53(5):1205–1207. doi: 10.1093/jnci/53.5.1205. [DOI] [PubMed] [Google Scholar]
  39. Tinoco I., Jr, Borer P. N., Dengler B., Levin M. D., Uhlenbeck O. C., Crothers D. M., Bralla J. Improved estimation of secondary structure in ribonucleic acids. Nat New Biol. 1973 Nov 14;246(150):40–41. doi: 10.1038/newbio246040a0. [DOI] [PubMed] [Google Scholar]
  40. Wang J. C. Cyclization of coliphage 186 DNA. J Mol Biol. 1967 Sep 28;28(3):403–411. doi: 10.1016/s0022-2836(67)80089-5. [DOI] [PubMed] [Google Scholar]
  41. Wang J. C., Davidson N. Thermodynamic and kinetic studies on the interconversion between the linear and circular forms of phage lambda DNA. J Mol Biol. 1966 Jan;15(1):111–123. doi: 10.1016/s0022-2836(66)80213-9. [DOI] [PubMed] [Google Scholar]
  42. Wold W. S., Mackey J. K., Brackmann K. H., Takemori N., Rigden P., Green M. Analysis of human tumors and human malignant cell lines for BK virus-specific DNA sequences. Proc Natl Acad Sci U S A. 1978 Jan;75(1):454–458. doi: 10.1073/pnas.75.1.454. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Wu R., Taylor E. Nucleotide sequence analysis of DNA. II. Complete nucleotide sequence of the cohesive ends of bacteriophage lambda DNA. J Mol Biol. 1971 May 14;57(3):491–511. doi: 10.1016/0022-2836(71)90105-7. [DOI] [PubMed] [Google Scholar]
  44. Yang R. C., Wu R. BK virus DNA sequence coding for the amino-terminus of the T-antigen. Virology. 1979 Jan 30;92(2):340–352. doi: 10.1016/0042-6822(79)90139-9. [DOI] [PubMed] [Google Scholar]
  45. Yang R. C., Wu R. BK virus DNA sequence: extent of homology with simian virus 40 DNA. Proc Natl Acad Sci U S A. 1979 Mar;76(3):1179–1183. doi: 10.1073/pnas.76.3.1179. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Yang R. C., Wu R. BK virus DNA: cleavage map and sequence analysis. Proc Natl Acad Sci U S A. 1978 May;75(5):2150–2154. doi: 10.1073/pnas.75.5.2150. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. 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]
  48. Yang R. C., Wu R. Cleavage map of BK virus DNA with restriction endonucleases MboI and HaeIII. J Virol. 1978 Sep;27(3):700–712. doi: 10.1128/jvi.27.3.700-712.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Yang R. C., Wu R. Comparative study of papovavirus DNA: BKV(MM), BKV(WT) and SV40. Nucleic Acids Res. 1979 Oct 10;7(3):651–668. doi: 10.1093/nar/7.3.651. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Yang R. C., Wu R. Physical mapping of BK virus DNA with SacI, MboII, and AluI restriction endonucleases. J Virol. 1978 Dec;28(3):851–864. doi: 10.1128/jvi.28.3.851-864.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. van der Noordaa J. Infectivity, oncogenicity and transforming ability of BK virus and BK virus DNA. J Gen Virol. 1976 Mar;30(3):371–373. doi: 10.1099/0022-1317-30-3-371. [DOI] [PubMed] [Google Scholar]

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