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. 1995 Dec;69(12):7559–7569. doi: 10.1128/jvi.69.12.7559-7569.1995

High-resolution mapping of the human T-cell leukemia virus type 1 Rex-binding element by in vitro selection.

S Baskerville 1, M Zapp 1, A D Ellington 1
PMCID: PMC189694  PMID: 7494262

Abstract

Interactions between the Rex protein of HTLV-1 and the genomic Rex-binding element (XBE) mediate the cytoplasmic transport of viral mRNAs. However, it is uncertain which RNA sequences and structures contribute to Rex recognition. A portion of the viral genome that spanned the XBE was partially randomized, and functional Rex-binding variants were selected. Alignment of selected Rex-binding sequences revealed positions that were functionally conserved between different molecules. A model is presented in which a subset of the selected residues are in direct contact with Rex. Positions that covaried with one another were also found. These covariations support a secondary-structural model in which a central paired stem is symmetrically flanked by two bulge loops. On the basis of this model, site-directed mutations of the XBE were constructed and each half molecule was found to bind independently to Rex. The functional residues and secondary structures in the XBE half molecules bear a remarkable resemblance to the transactivation response region element of HIV-1. Since the transactivation response region element is known to interact specifically with arginine residues in the Tat protein, these results suggest that the XBE binds to the arginine-rich RNA-binding domain of Rex in a similar manner. This model is supported by the selection data.

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Selected References

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  1. Ahmed Y. F., Hanly S. M., Malim M. H., Cullen B. R., Greene W. C. Structure-function analyses of the HTLV-I Rex and HIV-1 Rev RNA response elements: insights into the mechanism of Rex and Rev action. Genes Dev. 1990 Jun;4(6):1014–1022. doi: 10.1101/gad.4.6.1014. [DOI] [PubMed] [Google Scholar]
  2. Ballaun C., Farrington G. K., Dobrovnik M., Rusche J., Hauber J., Böhnlein E. Functional analysis of human T-cell leukemia virus type I rex-response element: direct RNA binding of Rex protein correlates with in vivo activity. J Virol. 1991 Aug;65(8):4408–4413. doi: 10.1128/jvi.65.8.4408-4413.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bartel D. P., Zapp M. L., Green M. R., Szostak J. W. HIV-1 Rev regulation involves recognition of non-Watson-Crick base pairs in viral RNA. Cell. 1991 Nov 1;67(3):529–536. doi: 10.1016/0092-8674(91)90527-6. [DOI] [PubMed] [Google Scholar]
  4. Bogerd H. P., Huckaby G. L., Ahmed Y. F., Hanly S. M., Greene W. C. The type I human T-cell leukemia virus (HTLV-I) Rex trans-activator binds directly to the HTLV-I Rex and the type 1 human immunodeficiency virus Rev RNA response elements. Proc Natl Acad Sci U S A. 1991 Jul 1;88(13):5704–5708. doi: 10.1073/pnas.88.13.5704. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Bogerd H. P., Tiley L. S., Cullen B. R. Specific binding of the human T-cell leukemia virus type I Rex protein to a short RNA sequence located within the Rex-response element. J Virol. 1992 Dec;66(12):7572–7575. doi: 10.1128/jvi.66.12.7572-7575.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Giver L., Bartel D., Zapp M., Pawul A., Green M., Ellington A. D. Selective optimization of the Rev-binding element of HIV-1. Nucleic Acids Res. 1993 Nov 25;21(23):5509–5516. doi: 10.1093/nar/21.23.5509. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Grassmann R., Berchtold S., Aepinus C., Ballaun C., Boehnlein E., Fleckenstein B. In vitro binding of human T-cell leukemia virus rex proteins to the rex-response element of viral transcripts. J Virol. 1991 Jul;65(7):3721–3727. doi: 10.1128/jvi.65.7.3721-3727.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Gröne M., Hoffmann E., Berchtold S., Cullen B. R., Grassmann R. A single stem-loop structure within the HTLV-1 Rex response element is sufficient to mediate Rex activity in vivo. Virology. 1994 Oct;204(1):144–152. doi: 10.1006/viro.1994.1518. [DOI] [PubMed] [Google Scholar]
  9. Hanly S. M., Rimsky L. T., Malim M. H., Kim J. H., Hauber J., Duc Dodon M., Le S. Y., Maizel J. V., Cullen B. R., Greene W. C. Comparative analysis of the HTLV-I Rex and HIV-1 Rev trans-regulatory proteins and their RNA response elements. Genes Dev. 1989 Oct;3(10):1534–1544. doi: 10.1101/gad.3.10.1534. [DOI] [PubMed] [Google Scholar]
  10. Inoue J., Yoshida M., Seiki M. Transcriptional (p40x) and post-transcriptional (p27x-III) regulators are required for the expression and replication of human T-cell leukemia virus type I genes. Proc Natl Acad Sci U S A. 1987 Jun;84(11):3653–3657. doi: 10.1073/pnas.84.11.3653. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Leclerc F., Cedergren R., Ellington A. D. A three-dimensional model of the Rev-binding element of HIV-1 derived from analyses of aptamers. Nat Struct Biol. 1994 May;1(5):293–300. doi: 10.1038/nsb0594-293. [DOI] [PubMed] [Google Scholar]
  12. Lee S. W., Gallardo H. F., Gilboa E., Smith C. Inhibition of human immunodeficiency virus type 1 in human T cells by a potent Rev response element decoy consisting of the 13-nucleotide minimal Rev-binding domain. J Virol. 1994 Dec;68(12):8254–8264. doi: 10.1128/jvi.68.12.8254-8264.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Lee T. C., Sullenger B. A., Gallardo H. F., Ungers G. E., Gilboa E. Overexpression of RRE-derived sequences inhibits HIV-1 replication in CEM cells. New Biol. 1992 Jan;4(1):66–74. [PubMed] [Google Scholar]
  14. Malim M. H., Hauber J., Le S. Y., Maizel J. V., Cullen B. R. The HIV-1 rev trans-activator acts through a structured target sequence to activate nuclear export of unspliced viral mRNA. Nature. 1989 Mar 16;338(6212):254–257. doi: 10.1038/338254a0. [DOI] [PubMed] [Google Scholar]
  15. Mattaj I. W. RNA recognition: a family matter? Cell. 1993 Jun 4;73(5):837–840. doi: 10.1016/0092-8674(93)90265-r. [DOI] [PubMed] [Google Scholar]
  16. Michel F., Ellington A. D., Couture S., Szostak J. W. Phylogenetic and genetic evidence for base-triples in the catalytic domain of group I introns. Nature. 1990 Oct 11;347(6293):578–580. doi: 10.1038/347578a0. [DOI] [PubMed] [Google Scholar]
  17. Puglisi J. D., Tan R., Calnan B. J., Frankel A. D., Williamson J. R. Conformation of the TAR RNA-arginine complex by NMR spectroscopy. Science. 1992 Jul 3;257(5066):76–80. doi: 10.1126/science.1621097. [DOI] [PubMed] [Google Scholar]
  18. Tan R., Chen L., Buettner J. A., Hudson D., Frankel A. D. RNA recognition by an isolated alpha helix. Cell. 1993 Jun 4;73(5):1031–1040. doi: 10.1016/0092-8674(93)90280-4. [DOI] [PubMed] [Google Scholar]
  19. Toyoshima H., Itoh M., Inoue J., Seiki M., Takaku F., Yoshida M. Secondary structure of the human T-cell leukemia virus type 1 rex-responsive element is essential for rex regulation of RNA processing and transport of unspliced RNAs. J Virol. 1990 Jun;64(6):2825–2832. doi: 10.1128/jvi.64.6.2825-2832.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Tuerk C., Gold L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science. 1990 Aug 3;249(4968):505–510. doi: 10.1126/science.2200121. [DOI] [PubMed] [Google Scholar]
  21. Tuerk C., MacDougal-Waugh S. In vitro evolution of functional nucleic acids: high-affinity RNA ligands of HIV-1 proteins. Gene. 1993 Dec 27;137(1):33–39. doi: 10.1016/0378-1119(93)90248-2. [DOI] [PubMed] [Google Scholar]
  22. Unge T., Solomin L., Mellini M., Derse D., Felber B. K., Pavlakis G. N. The Rex regulatory protein of human T-cell lymphotropic virus type I binds specifically to its target site within the viral RNA. Proc Natl Acad Sci U S A. 1991 Aug 15;88(16):7145–7149. doi: 10.1073/pnas.88.16.7145. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Weeks K. M., Ampe C., Schultz S. C., Steitz T. A., Crothers D. M. Fragments of the HIV-1 Tat protein specifically bind TAR RNA. Science. 1990 Sep 14;249(4974):1281–1285. doi: 10.1126/science.2205002. [DOI] [PubMed] [Google Scholar]
  24. Weeks K. M., Crothers D. M. RNA recognition by Tat-derived peptides: interaction in the major groove? Cell. 1991 Aug 9;66(3):577–588. doi: 10.1016/0092-8674(81)90020-9. [DOI] [PubMed] [Google Scholar]
  25. Yoshida M., Miyoshi I., Hinuma Y. Isolation and characterization of retrovirus from cell lines of human adult T-cell leukemia and its implication in the disease. Proc Natl Acad Sci U S A. 1982 Mar;79(6):2031–2035. doi: 10.1073/pnas.79.6.2031. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Zon G., Gallo K. A., Samson C. J., Shao K. L., Summers M. F., Byrd R. A. Analytical studies of 'mixed sequence' oligodeoxyribonucleotides synthesized by competitive coupling of either methyl- or beta-cyanoethyl-N,N-diisopropylamino phosphoramidite reagents, including 2'-deoxyinosine. Nucleic Acids Res. 1985 Nov 25;13(22):8181–8196. doi: 10.1093/nar/13.22.8181. [DOI] [PMC free article] [PubMed] [Google Scholar]

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