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. 1996 Aug;70(8):4986–4995. doi: 10.1128/jvi.70.8.4986-4995.1996

Identification and characterization of a hepatitis delta virus RNA transcriptional promoter.

M R Beard 1, T B MacNaughton 1, E J Gowans 1
PMCID: PMC190452  PMID: 8764005

Abstract

Transcription and replication of hepatitis delta virus (HDV) RNA are performed by the cellular enzyme RNA polymerase II (Pol II). As DNA is the normal template for Pol II, the enzyme must undergo template switching. The mechanism for this is unknown, but since HDV RNA can form a rod-like molecule by extensive intramolecular base pairing, it has been suggested that a double-stranded region(s) of HDV RNA serves as a recognition site for Pol II. A bidirectional promoter has been identified previously on HDV cDNA (T. B. Macnaughton, M. R. Beard, M. Chao, E. J. Gowans, and M. M. C. Lai, Virology 196:629-636, 1993). In the present study, genomic RNA corresponding to this region was able to direct the synthesis of antigenomic RNA in a nuclear extract transcription reaction, whereas genomic RNA species containing a mutation that resulted in a replication-defective phenotype were unable to do so. Thus, this region, the location of which is defined as nucleotides 1608 to 1669 on the basis of a highly conserved structure, represents a RNA-RNA promoter. Computer analysis of the RNA secondary structure predicted that the promoter contains two bulge regions in a stem-loop structure which encompasses a GC-rich motif. This predicted model was confirmed by enzyme digestion and primer extension analysis. The promoter is located at one end of the rod and has some homology with the simian virus 40 late promoter. A number of other mutations were introduced within this region, and expression plasmids were constructed to examine the effects of mutations in the promoter on HDV replication. Disruption of the overall secondary structure, particularly the bulge regions, totally inhibited HDV RNA replication.

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Selected References

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  1. Ali N., Siddiqui A. Interaction of polypyrimidine tract-binding protein with the 5' noncoding region of the hepatitis C virus RNA genome and its functional requirement in internal initiation of translation. J Virol. 1995 Oct;69(10):6367–6375. doi: 10.1128/jvi.69.10.6367-6375.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bartenschlager R., Schaller H. Hepadnaviral assembly is initiated by polymerase binding to the encapsidation signal in the viral RNA genome. EMBO J. 1992 Sep;11(9):3413–3420. doi: 10.1002/j.1460-2075.1992.tb05420.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Berkhout B., Jeang K. T. trans activation of human immunodeficiency virus type 1 is sequence specific for both the single-stranded bulge and loop of the trans-acting-responsive hairpin: a quantitative analysis. J Virol. 1989 Dec;63(12):5501–5504. doi: 10.1128/jvi.63.12.5501-5504.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Casey J. L., Bergmann K. F., Brown T. L., Gerin J. L. Structural requirements for RNA editing in hepatitis delta virus: evidence for a uridine-to-cytidine editing mechanism. Proc Natl Acad Sci U S A. 1992 Aug 1;89(15):7149–7153. doi: 10.1073/pnas.89.15.7149. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Casey J. L., Brown T. L., Colan E. J., Wignall F. S., Gerin J. L. A genotype of hepatitis D virus that occurs in northern South America. Proc Natl Acad Sci U S A. 1993 Oct 1;90(19):9016–9020. doi: 10.1073/pnas.90.19.9016. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Casey J. L., Gerin J. L. Hepatitis D virus RNA editing: specific modification of adenosine in the antigenomic RNA. J Virol. 1995 Dec;69(12):7593–7600. doi: 10.1128/jvi.69.12.7593-7600.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Chang F. L., Chen P. J., Tu S. J., Wang C. J., Chen D. S. The large form of hepatitis delta antigen is crucial for assembly of hepatitis delta virus. Proc Natl Acad Sci U S A. 1991 Oct 1;88(19):8490–8494. doi: 10.1073/pnas.88.19.8490. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Chao Y. C., Chang M. F., Gust I., Lai M. M. Sequence conservation and divergence of hepatitis delta virus RNA. Virology. 1990 Oct;178(2):384–392. doi: 10.1016/0042-6822(90)90335-o. [DOI] [PubMed] [Google Scholar]
  9. Chao Y. C., Lee C. M., Tang H. S., Govindarajan S., Lai M. M. Molecular cloning and characterization of an isolate of hepatitis delta virus from Taiwan. Hepatology. 1991 Feb;13(2):345–352. [PubMed] [Google Scholar]
  10. Chen P. J., Kalpana G., Goldberg J., Mason W., Werner B., Gerin J., Taylor J. Structure and replication of the genome of the hepatitis delta virus. Proc Natl Acad Sci U S A. 1986 Nov;83(22):8774–8778. doi: 10.1073/pnas.83.22.8774. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Ellis L., Clauser E., Morgan D. O., Edery M., Roth R. A., Rutter W. J. Replacement of insulin receptor tyrosine residues 1162 and 1163 compromises insulin-stimulated kinase activity and uptake of 2-deoxyglucose. Cell. 1986 Jun 6;45(5):721–732. doi: 10.1016/0092-8674(86)90786-5. [DOI] [PubMed] [Google Scholar]
  12. Feng S., Holland E. C. HIV-1 tat trans-activation requires the loop sequence within tar. Nature. 1988 Jul 14;334(6178):165–167. doi: 10.1038/334165a0. [DOI] [PubMed] [Google Scholar]
  13. Fu T. B., Taylor J. The RNAs of hepatitis delta virus are copied by RNA polymerase II in nuclear homogenates. J Virol. 1993 Dec;67(12):6965–6972. doi: 10.1128/jvi.67.12.6965-6972.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Geng Y., Johnson L. F. Lack of an initiator element is responsible for multiple transcriptional initiation sites of the TATA-less mouse thymidylate synthase promoter. Mol Cell Biol. 1993 Aug;13(8):4894–4903. doi: 10.1128/mcb.13.8.4894. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Gowans E. J., Baroudy B. M., Negro F., Ponzetto A., Purcell R. H., Gerin J. L. Evidence for replication of hepatitis delta virus RNA in hepatocyte nuclei after in vivo infection. Virology. 1988 Nov;167(1):274–278. doi: 10.1016/0042-6822(88)90078-5. [DOI] [PubMed] [Google Scholar]
  16. Hellen C. U., Witherell G. W., Schmid M., Shin S. H., Pestova T. V., Gil A., Wimmer E. A cytoplasmic 57-kDa protein that is required for translation of picornavirus RNA by internal ribosomal entry is identical to the nuclear pyrimidine tract-binding protein. Proc Natl Acad Sci U S A. 1993 Aug 15;90(16):7642–7646. doi: 10.1073/pnas.90.16.7642. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Hsieh S. Y., Chao M., Coates L., Taylor J. Hepatitis delta virus genome replication: a polyadenylated mRNA for delta antigen. J Virol. 1990 Jul;64(7):3192–3198. doi: 10.1128/jvi.64.7.3192-3198.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Imazeki F., Omata M., Ohto M. Complete nucleotide sequence of hepatitis delta virus RNA in Japan. Nucleic Acids Res. 1991 Oct 11;19(19):5439–5439. doi: 10.1093/nar/19.19.5439. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Jaeger J. A., Turner D. H., Zuker M. Improved predictions of secondary structures for RNA. Proc Natl Acad Sci U S A. 1989 Oct;86(20):7706–7710. doi: 10.1073/pnas.86.20.7706. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Jaeger J. A., Turner D. H., Zuker M. Predicting optimal and suboptimal secondary structure for RNA. Methods Enzymol. 1990;183:281–306. doi: 10.1016/0076-6879(90)83019-6. [DOI] [PubMed] [Google Scholar]
  21. Javahery R., Khachi A., Lo K., Zenzie-Gregory B., Smale S. T. DNA sequence requirements for transcriptional initiator activity in mammalian cells. Mol Cell Biol. 1994 Jan;14(1):116–127. doi: 10.1128/mcb.14.1.116. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Jilbert A. R., Gowans E. J., Macnaughton T. B., Burrell C. J. Characterization of a subgenomic HDV-specific poly(A)+ RNA species isolated from human hepatoma cells supporting HDV RNA replication. Prog Clin Biol Res. 1991;364:309–314. [PubMed] [Google Scholar]
  23. Kos A., Dijkema R., Arnberg A. C., van der Meide P. H., Schellekens H. The hepatitis delta (delta) virus possesses a circular RNA. Nature. 1986 Oct 9;323(6088):558–560. doi: 10.1038/323558a0. [DOI] [PubMed] [Google Scholar]
  24. Kuo M. Y., Chao M., Taylor J. Initiation of replication of the human hepatitis delta virus genome from cloned DNA: role of delta antigen. J Virol. 1989 May;63(5):1945–1950. doi: 10.1128/jvi.63.5.1945-1950.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Lee C. M., Bih F. Y., Chao Y. C., Govindarajan S., Lai M. M. Evolution of hepatitis delta virus RNA during chronic infection. Virology. 1992 May;188(1):265–273. doi: 10.1016/0042-6822(92)90756-f. [DOI] [PubMed] [Google Scholar]
  26. Liao W. C., Ash J., Johnson L. F. Bidirectional promoter of the mouse thymidylate synthase gene. Nucleic Acids Res. 1994 Oct 11;22(20):4044–4049. doi: 10.1093/nar/22.20.4044. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Luo G. X., Chao M., Hsieh S. Y., Sureau C., Nishikura K., Taylor J. A specific base transition occurs on replicating hepatitis delta virus RNA. J Virol. 1990 Mar;64(3):1021–1027. doi: 10.1128/jvi.64.3.1021-1027.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. MacNaughton T. B., Gowans E. J., McNamara S. P., Burrell C. J. Hepatitis delta antigen is necessary for access of hepatitis delta virus RNA to the cell transcriptional machinery but is not part of the transcriptional complex. Virology. 1991 Sep;184(1):387–390. doi: 10.1016/0042-6822(91)90855-6. [DOI] [PubMed] [Google Scholar]
  29. Macnaughton T. B., Beard M. R., Chao M., Gowans E. J., Lai M. M. Endogenous promoters can direct the transcription of hepatitis delta virus RNA from a recircularized cDNA template. Virology. 1993 Oct;196(2):629–636. doi: 10.1006/viro.1993.1519. [DOI] [PubMed] [Google Scholar]
  30. Macnaughton T. B., Gowans E. J., Jilbert A. R., Burrell C. J. Hepatitis delta virus RNA, protein synthesis and associated cytotoxicity in a stably transfected cell line. Virology. 1990 Aug;177(2):692–698. doi: 10.1016/0042-6822(90)90535-y. [DOI] [PubMed] [Google Scholar]
  31. Macnaughton T. B., Gowans E. J., Reinboth B., Jilbert A. R., Burrell C. J. Stable expression of hepatitis delta virus antigen in a eukaryotic cell line. J Gen Virol. 1990 Jun;71(Pt 6):1339–1345. doi: 10.1099/0022-1317-71-6-1339. [DOI] [PubMed] [Google Scholar]
  32. Macnaughton T. B., Wang Y. J., Lai M. M. Replication of hepatitis delta virus RNA: effect of mutations of the autocatalytic cleavage sites. J Virol. 1993 Apr;67(4):2228–2234. doi: 10.1128/jvi.67.4.2228-2234.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Makino S., Chang M. F., Shieh C. K., Kamahora T., Vannier D. M., Govindarajan S., Lai M. M. Molecular cloning and sequencing of a human hepatitis delta (delta) virus RNA. Nature. 1987 Sep 24;329(6137):343–346. doi: 10.1038/329343a0. [DOI] [PubMed] [Google Scholar]
  34. Pollack J. R., Ganem D. Site-specific RNA binding by a hepatitis B virus reverse transcriptase initiates two distinct reactions: RNA packaging and DNA synthesis. J Virol. 1994 Sep;68(9):5579–5587. doi: 10.1128/jvi.68.9.5579-5587.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Smale S. T., Baltimore D. The "initiator" as a transcription control element. Cell. 1989 Apr 7;57(1):103–113. doi: 10.1016/0092-8674(89)90176-1. [DOI] [PubMed] [Google Scholar]
  36. Tai F. P., Chen P. J., Chang F. J., Chen D. S. Hepatitis delta virus cDNA monomer can be used in transfection experiments to initiate viral RNA replication. Virology. 1993 Nov;197(1):137–142. doi: 10.1006/viro.1993.1574. [DOI] [PubMed] [Google Scholar]
  37. Wang K. S., Choo Q. L., Weiner A. J., Ou J. H., Najarian R. C., Thayer R. M., Mullenbach G. T., Denniston K. J., Gerin J. L., Houghton M. Structure, sequence and expression of the hepatitis delta (delta) viral genome. Nature. 1986 Oct 9;323(6088):508–514. doi: 10.1038/323508a0. [DOI] [PubMed] [Google Scholar]
  38. Zheng H., Fu T. B., Lazinski D., Taylor J. Editing on the genomic RNA of human hepatitis delta virus. J Virol. 1992 Aug;66(8):4693–4697. doi: 10.1128/jvi.66.8.4693-4697.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Zuker M. On finding all suboptimal foldings of an RNA molecule. Science. 1989 Apr 7;244(4900):48–52. doi: 10.1126/science.2468181. [DOI] [PubMed] [Google Scholar]

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