Chapter 3 Replication of the Hepatitis Delta Virus RNA Genome

Advances in Virus Research

Volumn 74, Issue , 2009, Pages 103-121

  Taylor, John M ^a  

^a FOX CHASE CANCER CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HEPATITIS DELTA ANTIGEN; RNA DIRECTED RNA POLYMERASE; VIRUS RNA;

CELL NUCLEUS; GENETICS; HEPATITIS B VIRUS; HEPATITIS DELTA VIRUS; HUMAN; METABOLISM; PLANT; REVIEW; VIROLOGY; VIRUS GENOME; VIRUS REPLICATION;

CELL NUCLEUS; GENOME, VIRAL; HEPATITIS B VIRUS; HEPATITIS DELTA ANTIGENS; HEPATITIS DELTA VIRUS; HUMANS; PLANTS; RNA REPLICASE; RNA, VIRAL; VIRUS REPLICATION;

EID: 68649120681     PISSN: 00653527     EISSN: 15578399     Source Type: Book Series    
DOI: 10.1016/S0065-3527(09)74003-5     Document Type: Review

References (84)

1. Abrahem A., and Pelchat M. Formation of an RNA polymerase II preinitiation complex on an RNA promoter derived from the hepatitis delta virus RNA genome. Nucl. Acids Res. 36 (2008) 5201-5211
2. Alves C., Freitas N., and Cunha C. Characterization of the nuclear localization signal of the hepatitis delta virus antigen. Virology 370 (2008) 12-21
3. Beard M.R., Macnaughton T.B., and Gowans E.J. Identification and characterization of a hepatitis delta virus RNA transcriptional promoter. J. Virol. 70 (1996) 4986-4995
4. Bichko V.V., and Taylor J.M. Redistribution of the delta antigens in cells replicating the genome of hepatitis delta virus. J. Virol. 70 (1996) 8064-8070
5. Branch A.D., and Robertson H.D. A replication cycle for viroids and small infectious RNAs. Science 223 (1984) 450-455
6. Branch A.D., Levine B.J., and Robertson H.D. The brotherhood of circular RNA pathogens: Viroids, circular satellites, and the delta agent. Semin. Virol. 1 (1990) 143-152
7. Brazas R., and Ganem D. A cellular homolog of hepatitis delta antigen: Implications for viral replication and evolution. Science 274 (1996) 90-94
8. Butcher S.J., Grimes J.M., Makeyev E.V., Bamford D.H., and Stuart D.I. A mechanism for initiating RNA-dependent RNA polymerization. Nature 410 (2001) 235-240
9. Casey J.L. Hepatitis delta virus. In: Compans R.M., Cooper M.D., Honjo T., Koprowski H., Melchers F., Oldstone M.B.A., Olsnes S., Potter M., Vogt P.K., and Wagner H. (Eds). Current Topics in Microbiology and Immunology Vol. 307 (2006), Springer, Berlin
10. Casey J.L. Hepatitis delta virus RNA editing. In: Handa H., and Yamaguchi Y. (Eds). Hepatitis Delta Virus (2006), Landes Bioscience, Georgetown, TX 52-65
11. Chang J., and Taylor J. In vivo RNA-directed transcription, with template switching, by a mammalian RNA polymerase. EMBO J. 21 (2002) 157-164
12. Chang M.-F., Baker S.C., Soe L.H., Kamahora T., Keck J.G., Makino S., Govindarajan S., and Lai M.M.C. Human hepatitis delta antigen is a nuclear phosphoprotein with RNA binding activity. J. Virol. 62 (1988) 2403-2410
13. Chang F.L., Chen P.J., Tu S.J., Chiu M.N., Wang C.J., and Chen D.S. The large form of hepatitis d antigen is crucial for the assembly of hepatitis d virus. Proc. Natl. Acad. Sci. USA 88 (1991) 8490-8494
14. Chang J., Nie X., Gudima S., and Taylor J. Action of inhibitors on accumulation of processed hepatitis delta virus RNAs. J. Virol. 80 (2006) 3205-3214
15. Chang J., Nie X., Chang H.E., Han Z., and Taylor J. Transcription of hepatitis delta virus RNA by RNA polymerase II. J. Virol. 82 (2008) 1118-1127
16. Chao M. RNA recombination in hepatitis delta virus: Implications regarding the abilities of mammalian RNA polymerases. Virus Res. 127 (2007) 208-215
17. Chao M., Hsieh S.-Y., and Taylor J. Role of two forms of the hepatitis delta virus antigen: Evidence for a mechanism of self-limiting genome replication. J. Virol. 64 (1990) 5066-5069
18. Chao M., Hsieh S.-Y., and Taylor J. The antigen of hepatitis delta virus: Examination of in vitro RNA-binding specificity. J. Virol. 65 (1991) 4057-4062
19. Chao M., Wang T.C., and Lee S.E. Detection of hepatitis delta virus recombinants in cultured cells co-transfected with cloned genotypes I and IIb DNA sequences. J. Virol. Methods 137 (2006) 252-258
20. Chen P.-J., Kalpana G., Goldberg J., Mason W., Werner B., Gerin J., and Taylor J. Structure and replication of the genome of hepatitis d virus. Proc. Natl. Acad. Sci. USA 83 (1986) 8774-8778
21. Chou H.C., Hsieh T.Y., Sheu G.T., and Lai M.M. Hepatitis delta antigen mediates the nuclear import of hepatitis delta virus RNA. J. Virol. 72 (1998) 3684-3690
22. Daros J.A., Elena S.F., and Flores R. Viroids: An Ariadne's thread into the RNA labyrinth. EMBO Rep. 7 (2006) 593-598
23. Defenbaugh D.A., Johnson M., Chen R., Zheng Y.Y., and Casey J.L. Hepatitis delta antigen requires a minimum length of the hepatitis delta virus unbranched rod RNA structure for binding. J. Virol. 83 (2009) 4548-4556
24. Deny P. Hepatitis delta virus genetic variability: From genotypes I, II, III to eight major clades. In: Casey J.L. (Ed). Hepatitis Delta Virus (2006), Springer, Heidelberg 151-171
25. Doudna J.A., and Lorsch J.R. Ribozyme catalysis: Not different, just worse. Nat. Struct. Mol. Biol. 12 (2005) 395-402
26. Enomoto N., Watanabe H., Nagayama K., Yamashiro T., and Watanabe M. Genotype of hepatitis delta virus. In: Handa H., and Yamaguchi Y. (Eds). Hepatitis Delta Virus (2006), Landes Bioscience, Georgetown, TX 1-9
27. Filipovska J., and Konarska M.M. Specific HDV RNA-templated transcription by pol II in vitro. RNA 6 (2000) 41-54
28. Flores R., Gas M.E., Molina D., Hernandez C., and Daros J.A. Analysis of viroid replication. Methods Mol. Biol. 451 (2008) 167-183
29. Fu T.-B., and Taylor J. The RNAs of hepatitis delta virus are copied by RNA polymerase II in nuclear homogenates. J. Virol. 67 (1993) 6965-6972
30. Glenn J.S., Taylor J.M., and White J.M. In vitro-synthesized hepatitis delta virus RNA initiates genome replication in cultured cells. J. Virol. 64 (1990) 3104-3107
31. Glenn J.S., Watson J.A., Havel C.M., and White J.O. Identification of a prenylation site in the delta virus large antigen. Science 256 (1992) 1331-1333
32. Goh G.K., Dunker A.K., and Uversky V.N. A comparative analysis of viral matrix proteins using disorder predictors. Virol. J. 5 (2008) 126
33. Goh G.K., Dunker A.K., and Uversky V.N. Protein intrinsic disorder toolbox for comparative analysis of viral proteins. BMC Genomics 9 Suppl. 2 (2008) S4
34. Greco-Stewart V.S., Miron P., Abrahem A., and Pelchat M. The human RNA polymerase II interacts with the terminal stem-loop regions of the hepatitis delta virus RNA genome. Virology 357 (2007) 68-78
35. Greco-Stewart V.S., Schissel E., and Pelchat M. The hepatitis delta virus RNA genome interacts with the human RNA polymerases I and III. Virology 386 (2009) 12-15
36. Gudima S., Dingle K., Wu T.-T., Moraleda G., and Taylor J. Characterization of the 5′-ends for polyadenylated RNAs synthesized during the replication of hepatitis delta virus. J. Virol. 73 (1999) 6533-6539
37. Gudima S., Wu S.-Y., Chiang C.-M., Moraleda G., and Taylor J. Origin of the hepatitis delta virus mRNA. J. Virol. 74 (2000) 7204-7210
38. Gudima S.O., Chang J., and Taylor J.M. Reconstitution in cultured cells of replicating HDV RNA from pairs of less than full-length RNAs. RNA 11 (2005) 90-98
39. Han Z., Alves C., Gudima S., and Taylor J. Intracellular localization of hepatitis delta virus proteins in the presence and absence of viral RNA accumulation. J. Virol. 83 (2009) 6457-6463
40. In: Handa H., and Yamaguchi Y. (Eds). Hepatitis Delta Virus (2006), Landes Bioscience, Georgetown, TX
41. Haussecker D., Cao D., Huang Y., Parameswaran P., Fire A.Z., and Kay M.A. Capped small RNAs and MOV10 in human hepatitis delta virus replication. Nat. Struct. Mol. Biol. 15 (2008) 714-721
42. Huang Z.S., and Wu H.N. Identification and characterization of the RNA chaperone activity of hepatitis delta antigen peptides. J. Biol. Chem. 273 (1998) 26455-26461
43. Huang W.H., Yung B.Y., Syu W.J., and Lee Y.H. The nucleolar phosphoprotein B23 interacts with hepatitis delta antigens and modulates the hepatitis delta virus RNA replication. J. Biol. Chem. 276 (2001) 25166-25175
44. Kuo M.Y.-P., Goldberg J., Coates L., Mason W., Gerin J., and Taylor J. Molecular cloning of hepatitis delta virus RNA from an infected woodchuck liver: Sequence, structure, and applications. J. Virol. 62 (1988) 1855-1861
45. Kuo M.Y.P., Sharmeen L., Dinter-Gottlieb G., and Taylor J. Characterization of self-cleaving RNA sequences on the genome and antigenome of human hepatitis delta virus. J. Virol. 62 (1988) 4439-4444
46. Lai M.M. RNA replication without RNA-dependent RNA polymerase: Surprises from hepatitis delta virus. J. Virol. 79 (2005) 7951-7958
47. Lai M.M.C. Hepatitis delta antigen: Biochemical properties and functional roles in HDV replication. In: Handa H., and Yamaguchi Y. (Eds). Hepatitis Delta Virus (2006), Landes Bioscience, Georgetown, TX 38-51
48. Laurila M.R., Salgado P.S., Stuart D.I., Grimes J.M., and Bamford D.H. Back-priming mode of phi6 RNA-dependent RNA polymerase. J. Gen. Virol. 86 (2005) 521-526
49. Lazinski D.W., and Taylor J.M. Intracellular cleavage and ligation of hepatitis delta virus genomic RNA: Regulation of ribozyme activity by cis-acting sequences and host factors. J. Virol. 69 (1995) 1190-1200
50. Lee C.-H., Chang S.C., Chen C.-J., and Chang M.-F. The nucleolin binding activity of hepatitis delta antigen is associated with nucleolus targeting. J. Biol. Chem. 273 (1998) 7650-7656
51. Lehmann E., Brueckner F., and Cramer P. Molecular basis of RNA-dependent RNA polymerase II activity. Nature 450 (2007) 445-449
52. Li Y.J., Macnaughton T., Gao L., and Lai M.M. RNA-templated replication of hepatitis delta virus: Genomic and antigenomic RNAs associate with different nuclear bodies. J. Virol. 80 (2006) 6478-6486
53. Linnstaedt S.D., Kasprzak W.K., Shapiro B.A., and Casey J.L. The fraction of RNA that folds into the correct branched secondary structure determines hepatitis delta virus type 3 RNA editing levels. RNA 15 (2009) 1177-1187
54. Macnaughton T.B., and Lai M.M. Genomic but not antigenomic hepatitis delta virus RNA is preferentially exported from the nucleus immediately after synthesis and processing. J. Virol. 76 (2002) 3928-3935
55. Macnaughton T.B., Beard M.R., Chao M., Gowans E.J., and Lai M.M.C. Endogenous promoters can direct the transcription of hepatitis delta virus RNA from a recircularized cDNA template. Virology 196 (1993) 629-636
56. Macnaughton T.B., Shi S.T., Modahl L.E., and Lai M.M. Rolling circle replication of hepatitis delta virus RNA is carried out by two different cellular RNA polymerases. J. Virol. 76 (2002) 3920-3927
57. Modahl L.E., Macnaughton T.B., Zhu N., Johnson D.L., and Lai M.M.C. RNA-dependent replication and transcription of hepatitis delta virus RNA involve distinct cellular RNA polymerases. Mol. Cell. Biol. 20 (2000) 6030-6039
58. Moraleda G., and Taylor J. Host RNA polymerase requirements for transcription of the human hepatitis delta virus genome. J. Virol. 75 (2001) 10161-10169
59. Nedialkov Y.A., Gong X.Q., Hovde S.L., Yamaguchi Y., Handa H., Geiger J.H., Yan H., and Burton Z.F. NTP-driven translocation by human RNA polymerase II. J. Biol. Chem. 278 (2003) 18303-18312
60. Nie X., Chang J., and Taylor J.M. Alternative processing of hepatitis delta virus antigenomic RNA transcripts. J. Virol. 78 (2004) 4517-4524
61. Pelchat M., Grenier C., and Perreault J.P. Characterization of a viroid-derived RNA promoter for the DNA-dependent RNA polymerase from Escherichia coli. Biochemistry 41 (2002) 6561-6571
62. Perrotta A.T., and Been M.D. A single nucleotide linked to a switch in metal ion reactivity preference in the HDV ribozymes. Biochemistry 46 (2007) 5124-5130
63. Preker P., Nielsen J., Kammler S., Lykke-Andersen S., Christensen M.S., Mapendano C.K., Schierup M.H., and Jensen T.H. RNA exosome depletion reveals transcription upstream of active human promoters. Science 322 (2008) 1851-1854
64. Radjef N., Gordien E., Ivaniushina V., Gault E., Anais P., Drugan T., Trinchet J.C., Roulot D., Tamby M., Milinkovitch M.C., and Deny P. Molecular phylogenetic analyses indicate a wide and ancient radiation of African hepatitis delta virus, suggesting a deltavirus genus of at least seven major clades. J. Virol. 78 (2004) 2537-2544
65. Rizzetto M., Canese M.G., Arico J., Crivelli O., Bonino F., Trepo C.G., and Verme G. Immunofluorescence detection of a new antigen-antibody system associated to the hepatitis B virus in the liver and in the serum of HBsAg carriers. Gut 18 (1977) 997-1003
66. 2+ inhibition of an RNA-dependent RNA polymerase. Structure 12 (2004) 307-316
67. Sharmeen L., Kuo M.Y., Dinter-Gottlieb G., and Taylor J. The antigenomic RNA of human hepatitis delta virus can undergo self-cleavage. J. Virol. 62 (1988) 2674-2679
68. Sureau C. The role of the HBV envelope proteins in the HDV replication cycle. Curr. Top. Microbiol. Immunol. 307 (2006) 113-131
69. Tabler M., and Tsagris M. Viroids: Petite RNA pathogens with distinguished talents. Trends Plant Sci. 9 (2004) 339-348
70. Taft R.J., Glazov E.A., Cloonan N., Simons C., Stephen S., Faulkner G.J., Lassmann T., Forrest A.R., Grimmond S.M., Schroder K., Irvine K., Arakawa T., et al. Tiny RNAs associated with transcription start sites in animals. Nat. Genet. 41 (2009) 572-578
71. Tavanez J.P., Cunha C., Silva M.C.A., David E., Monjardino J., and Carma-Fonseca M. Hepatitis delta virus ribonucleoproteins shuttle between the nucleus and the cytoplasm. RNA 8 (2002) 637-646
72. Taylor J.M. Hepatitis delta virus. Virology 344 (2006) 71-76
73. Taylor J., Mason W., Summers J., Goldberg J., Aldrich C., Coates L., Gerin J., and Gowans E. Replication of human hepatitis delta virus in primary cultures of woodchuck hepatocytes. J. Virol. 61 (1987) 2891-2895
74. Taylor J.M., Farci P., and Purcell R.H. Hepatitis D (delta) virus. In: Knipe D.M. (Ed). Fields Virology. 5 edn. (2007), Lippincott Williams & Wilkins, Philadelphia 3031-3046
75. Tseng C.H., Jeng K.S., and Lai M.M. Transcription of subgenomic mRNA of hepatitis delta virus requires a modified hepatitis delta antigen, distinct from antigenomic RNA synthesis. J. Virol. 82 (2008) 9409-9416
76. Urban S. New insights into hepatitis B and hepatitis delta virus entry. Future Virol. 3 (2008) 253-264
77. Wang T.C., and Chao M. RNA recombination of hepatitis delta virus in natural mixed-genotype infection and transfected cultured cells. J. Virol. 79 (2005) 2221-2229
78. Wu T.T., Netter H.J., Lazinski D.W., and Taylor J.M. Effects of nucleotide changes on the ability of hepatitis delta virus to transcribe, process, and accumulate unit-length, circular RNA. J. Virol. 71 (1997) 5408-5414
79. In: Yamaguchi K., and Handa H. (Eds). Hepatitis Delta Antigen and RNA Polymerase II (2006), Landes Bioscience, Georgetown, TX
80. Yamaguchi Y., Wada T., and Handa H. Interplay between positive and negative elongation factors: Drawing a new view of DRB. Genes Cells 3 (1998) 9-15
81. Yamaguchi Y., Filipovska J., Yano K., Furuya A., Inukai N., Narita T., Wada T., Sugimoto S., Konarska M.M., and Handa H. Stimulation of RNA polymerase II elongation by hepatitis delta antigen. Science 293 (2001) 124-127
82. Yamaguchi Y., Delehouzee S., and Handa H. HIV and hepatitis delta virus: Evolution takes different paths to relieve blocks in transcriptional elongation. Microbes Infect. 4 (2002) 1169-1175
83. Yamaguchi Y., Mura T., Chanarat S., Okamoto S., and Handa H. Hepatitis delta antigen binds to the clamp of RNA polymerase II and affects transcriptional fidelity. Genes Cells 12 (2007) 863-875
84. Zuccola H.J., Rozzelle J.E., Lemon S.M., Erickson B.W., and Hogle J.M. Structural basis of the oligomerization of hepatitis delta antigen. Structure 6 (1998) 821-830