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. 1991 Sep;65(9):5092–5095. doi: 10.1128/jvi.65.9.5092-5095.1991

Prevalence of the archetypal regulatory region and sequence polymorphisms in nonpassaged BK virus variants.

M Negrini 1, S Sabbioni 1, R R Arthur 1, A Castagnoli 1, G Barbanti-Brodano 1
PMCID: PMC248976  PMID: 1651425

Abstract

Since the first isolation and characterization of BK virus (BKV), a number of BKV variants which differ in genomic structure or antigenic determinants have been described. The regulatory region, in particular, the enhancer elements, show the most divergent sequences among different isolates. The structural organization of a putative ancestral prototype or archetype, from which all of the variants are probably derived, has been proposed. By sequencing the regulatory regions of 13 different isolates from the urine of bone marrow transplant recipients, we determined the structures and sequences of BKV variants diffused in the human population. The enhancer region was amplified by polymerase chain reaction to avoid passage in culture, and the product was directly sequenced. The structure most frequently observed is in agreement with the postulated archetype, containing a single enhancer element with no repeats. By sequence analysis we identified four hot spots of nucleotide variation. These variations are consistent with the existence of two consensus sequences. One sequence motif, observed in about 85% of the isolates, is referred to as the archetypal BKV, while a second motif, observed in the remaining 15% of the variants, is highly reminiscent of the AS strain.

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Selected References

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

  1. Arthur R. R., Dagostin S., Shah K. V. Detection of BK virus and JC virus in urine and brain tissue by the polymerase chain reaction. J Clin Microbiol. 1989 Jun;27(6):1174–1179. doi: 10.1128/jcm.27.6.1174-1179.1989. [DOI] [PMC free article] [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. Banerji J., Rusconi S., Schaffner W. Expression of a beta-globin gene is enhanced by remote SV40 DNA sequences. Cell. 1981 Dec;27(2 Pt 1):299–308. doi: 10.1016/0092-8674(81)90413-x. [DOI] [PubMed] [Google Scholar]
  4. 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]
  5. Corallini A., Pagnani M., Viadana P., Silini E., Mottes M., Milanesi G., Gerna G., Vettor R., Trapella G., Silvani V. Association of BK virus with human brain tumors and tumors of pancreatic islets. Int J Cancer. 1987 Jan 15;39(1):60–67. doi: 10.1002/ijc.2910390111. [DOI] [PubMed] [Google Scholar]
  6. Flaegstad T., Sundsfjord A., Arthur R. R., Pedersen M., Traavik T., Subramani S. Amplification and sequencing of the control regions of BK and JC virus from human urine by polymerase chain reaction. Virology. 1991 Feb;180(2):553–560. doi: 10.1016/0042-6822(91)90069-n. [DOI] [PubMed] [Google Scholar]
  7. 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]
  8. Gotoh O. An improved algorithm for matching biological sequences. J Mol Biol. 1982 Dec 15;162(3):705–708. doi: 10.1016/0022-2836(82)90398-9. [DOI] [PubMed] [Google Scholar]
  9. 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]
  10. Grinnell B. W., Berg D. T., Walls J. Activation of the adenovirus and BK virus late promoters: effects of the BK virus enhancer and trans-acting viral early proteins. Mol Cell Biol. 1986 Nov;6(11):3596–3605. doi: 10.1128/mcb.6.11.3596. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Gyllensten U. B., Erlich H. A. Generation of single-stranded DNA by the polymerase chain reaction and its application to direct sequencing of the HLA-DQA locus. Proc Natl Acad Sci U S A. 1988 Oct;85(20):7652–7656. doi: 10.1073/pnas.85.20.7652. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Hearing P., Shenk T. The adenovirus type 5 E1A transcriptional control region contains a duplicated enhancer element. Cell. 1983 Jul;33(3):695–703. doi: 10.1016/0092-8674(83)90012-0. [DOI] [PubMed] [Google Scholar]
  13. Maniatis T., Goodbourn S., Fischer J. A. Regulation of inducible and tissue-specific gene expression. Science. 1987 Jun 5;236(4806):1237–1245. doi: 10.1126/science.3296191. [DOI] [PubMed] [Google Scholar]
  14. Markowitz R. B., Tolbert S., Dynan W. S. Promoter evolution in BK virus: functional elements are created at sequence junctions. J Virol. 1990 May;64(5):2411–2415. doi: 10.1128/jvi.64.5.2411-2415.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Negrini M., Rimessi P., Mantovani C., Sabbioni S., Corallini A., Gerosa M. A., Barbanti-Brodano G. Characterization of BK virus variants rescued from human tumours and tumour cell lines. J Gen Virol. 1990 Nov;71(Pt 11):2731–2736. doi: 10.1099/0022-1317-71-11-2731. [DOI] [PubMed] [Google Scholar]
  16. 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]
  17. 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]
  18. Pustell J., Kafatos F. C. A convenient and adaptable package of computer programs for DNA and protein sequence management, analysis and homology determination. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):643–655. doi: 10.1093/nar/12.1part2.643. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. 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]
  20. Rubinstein R., Schoonakker B. C., Harley E. H. Recurring theme of changes in the transcriptional control region of BK virus during adaptation to cell culture. J Virol. 1991 Mar;65(3):1600–1604. doi: 10.1128/jvi.65.3.1600-1604.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. 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]
  22. Sugimoto C., Hara K., Taguchi F., Yogo Y. Growth efficiency of naturally occurring BK virus variants in vivo and in vitro. J Virol. 1989 Jul;63(7):3195–3199. doi: 10.1128/jvi.63.7.3195-3199.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Sundsfjord A., Johansen T., Flaegstad T., Moens U., Villand P., Subramani S., Traavik T. At least two types of control regions can be found among naturally occurring BK virus strains. J Virol. 1990 Aug;64(8):3864–3871. doi: 10.1128/jvi.64.8.3864-3871.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Tavis J. E., Frisque R. J., Walker D. L., White F. A., 3rd Antigenic and transforming properties of the DB strain of the human polyomavirus BK virus. Virology. 1990 Oct;178(2):568–572. doi: 10.1016/0042-6822(90)90355-u. [DOI] [PubMed] [Google Scholar]
  25. Tavis J. E., Walker D. L., Gardner S. D., Frisque R. J. Nucleotide sequence of the human polyomavirus AS virus, an antigenic variant of BK virus. J Virol. 1989 Feb;63(2):901–911. doi: 10.1128/jvi.63.2.901-911.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Watanabe S., Soeda E., Uchida S., Yoshiike K. DNA rearrangement affecting expression of the BK virus transforming gene. J Virol. 1984 Jul;51(1):1–6. doi: 10.1128/jvi.51.1.1-6.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. 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]
  28. Yogo Y., Kitamura T., Sugimoto C., Ueki T., Aso Y., Hara K., Taguchi F. Isolation of a possible archetypal JC virus DNA sequence from nonimmunocompromised individuals. J Virol. 1990 Jun;64(6):3139–3143. doi: 10.1128/jvi.64.6.3139-3143.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. 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]

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