Regulation of bovine papillomavirus type 1 gene expression by RNA processing

Frontiers in Bioscience

Volumn 14, Issue 4, 2009, Pages 1270-1282

  Jia, Rong ^a   Zheng, Zhi Ming ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

Author keywords

Gene expression; Papillomaviruses; Post transcriptional regulation; Review; RNA polyadenylation; RNA splicing

Indexed keywords

BOVINE PAPILLOMAVIRUS TYPE 1; PAPILLOMAVIRIDAE;

POLYADENYLIC ACID; VIRUS RNA;

BOVINE PAPILLOMAVIRUS TYPE 1; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; REVIEW; RNA PROCESSING; RNA SPLICING;

BOVINE PAPILLOMAVIRUS 1; GENE EXPRESSION REGULATION, VIRAL; POLY A; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA SPLICING; RNA, VIRAL;

EID: 63849254309     PISSN: 27686701     EISSN: 27686698     Source Type: Journal    
DOI: 10.2741/3307     Document Type: Article

References (84)

1. E. Y. Chen, P. M. Howley, A. D. Levinson & P. H. Seeburg, The primary structure and genetic organization of the bovine papillomavirus type 1 genome, Nature 299, 529-534 (1982).
2. Z. M. Zheng & C. C. Baker, Papillomavirus genome structure, expression, and post-transcriptional regulation, Front Biosci. 11, 2286-2302 (2006). (Pubitemid 43822560)
3. P. F. Lambert, B. A. Spalholz & P. M. Howley, A transcriptional repressor encoded by BPV-1 shares a common carboxy-terminal domain with the E2 transactivator, Cell 50, 69-78 (1987).
4. N. L. Hubbert, J. T. Schiller, D. R. Lowy & E. J. RNA processing and BPV-1 gene expression 1279 Androphy, Bovine papilloma virus-transformed cells contain multiple E2 proteins, Proc.Natl.Acad.Sci.U.S.A 85, 5864-5868 (1988).
5. J. Choe, P. Vaillancourt, A. Stenlund & M. Botchan, Bovine papillomavirus type 1 encodes two forms of a transcriptional repressor: structural and functional analysis of new viral cDNAs, J.Virol. 63, 1743-1755 (1989). (Pubitemid 19085989)
6. W. Waldeck, F. Rosl & H. Zentgraf, Origin of replication in episomal bovine papilloma virus type 1 DNA isolated from transformed cells, EMBO J. 3, 2173-2178 (1984).
7. M. Lusky & M. R. Botchan, Transient replication of bovine papilloma virus type 1 plasmids: cis and trans requirements, Proc.Natl.Acad.Sci.U.S.A 83, 3609-3613 (1986). (Pubitemid 16062334)
8. B. A. Spalholz, Y. C. Yang & P. M. Howley, Transactivation of a bovine papilloma virus transcriptional regulatory element by the E2 gene product, Cell 42, 183- 191 (1985). (Pubitemid 16237569)
9. B. A. Spalholz, P. F. Lambert, C. L. Yee & P. M. Howley, Bovine papillomavirus transcriptional regulation: localization of the E2-responsive elements of the long control region, J.Virol. 61, 2128-2137 (1987). (Pubitemid 17088923)
10. T. H. Haugen, T. P. Cripe, G. D. Ginder, M. Karin & L. P. Turek, Trans-activation of an upstream early gene promoter of bovine papilloma virus-1 by a product of the viral E2 gene, EMBO J. 6, 145-152 (1987).
11. S. M. Harrison, K. L. Gearing, S. Y. Kim, A. J. Kingsman & S. M. Kingsman, Multiple cis-active elements in the long control region of bovine papillomavirus type 1 (BPV-1), Nucleic Acids Res. 15, 10267-10284 (1987).
12. R. Li, J. Knight, G. Bream, A. Stenlund & M. Botchan, Specific recognition nucleotides and their DNA context determine the affinity of E2 protein for 17 binding sites in the BPV-1 genome, Genes Dev. 3, 510-526 (1989).
13. C. C. Baker & P. M. Howley, Differential promoter utilization by the bovine papillomavirus in transformed cells and productively infected wart tissues, EMBO J. 6, 1027-1035 (1987).
14. A. Stenlund, J. Zabielski, H. Ahola, J. Moreno-Lopez & U. Pettersson, Messenger RNAs from the transforming region of bovine papilloma virus type I, J.Mol.Biol. 182, 541-554 (1985). (Pubitemid 16223367)
15. Y. C. Yang, H. Okayama & P. M. Howley, Bovine papillomavirus contains multiple transforming genes, Proc.Natl.Acad.Sci.U.S.A 82, 1030-1034 (1985). (Pubitemid 15100488)
16. U. Linz & C. C. Baker, Promoters of bovine papillomavirus type 1: in vitro activity and utilization, J.Virol. 62, 2537-2543 (1988).
17. A. B. Sandler, C. C. Baker & B. A. Spalholz, Sp1 is critical for basal and E2-transactivated transcription from the bovine papillomavirus type 1 P89 promoter, J.Gen.Virol. 77, 189-198 (1996).
18. N. Jareborg, A. Alderborn & S. Burnett, Identification and genetic definition of a bovine papillomavirus type 1 E7 protein and absence of a low-copy-number phenotype exhibited by E5, E6, or E7 viral mutants, J.Virol. 66, 4957- 4965 (1992).
19. J. Bohl, B. Hull & S. B. Vande Pol, Cooperative transformation and coexpression of bovine papillomavirus type 1 E5 and E7 proteins, J.Virol. 75, 513-521 (2001).
20. P. L. Hermonat, B. A. Spalholz & P. M. Howley, The bovine papillomavirus P2443 promoter is E2 transresponsive: evidence for E2 autoregulation, EMBO J. 7, 2815-2822 (1988).
21. B. A. Spalholz, S. B. Vande Pol & P. M. Howley, Characterization of the cis elements involved in basal and E2-transactivated expression of the bovine papillomavirus P2443 promoter, J.Virol. 65, 743-753 (1991).
22. H. Ahola, A. Stenlund, J. Moreno-Lopez & U. Pettersson, Promoters and processing sites within the transforming region of bovine papillomavirus type 1, J.Virol. 61, 2240-2244 (1987). (Pubitemid 17088938)
23. P. F. Lambert, N. L. Hubbert, P. M. Howley & J. T. Schiller, Genetic assignment of multiple E2 gene products in bovine papillomavirus-transformed cells, J.Virol. 63, 3151-3154 (1989). (Pubitemid 19156038)
24. B. A. Spalholz, J. C. Byrne & P. M. Howley, Evidence for cooperativity between E2 binding sites in E2 transregulation of bovine papillomavirus type 1, J.Virol. 62, 3143-3150 (1988).
25. J. T. Schiller, E. Kleiner, E. J. Androphy, D. R. Lowy & H. Pfister, Identification of bovine papillomavirus E1 mutants with increased transforming and transcriptional activity, J.Virol. 63, 1775-1782 (1989). (Pubitemid 19085992)
26. S. K. Barksdale & C. C. Baker, Differentiation-specific expression from the bovine papillomavirus type 1 P2443 and late promoters, J.Virol. 67, 5605-5616 (1993). (Pubitemid 23241397)
27. H. Mishoe, J. N. Brady, M. Radonovich & N. P. Salzman, Simian virus 40 guanine-cytosine-rich sequences function as independent transcriptional control elements in vitro, Mol.Cell Biol. 4, 2911-2920 (1984). (Pubitemid 15106850)
28. J. Brady, M. Radonovich, M. Vodkin, V. Natarajan, M. Thoren, G. Das, J. Janik & N. P. Salzman, Site-specific base substitution and deletion mutations that enhance or suppress transcription of the SV40 major late RNA, Cell 31, 625-633 (1982). (Pubitemid 13223946)
29. S. Tang, M. Tao, J. P. McCoy Jr. & Z. M. Zheng, The E7 oncoprotein is translated from spliced E6*I transcripts in high-risk human papillomavirus type 16- or type 18 positive cervical cancer cell lines via translation reinitiation, J.Virol. 80, 4249-4263 (2006).
30. P. Vaillancourt, T. Nottoli, J. Choe & M. R. Botchan, The E2 transactivator of bovine papillomavirus type 1 is expressed from multiple promoters, J.Virol. 64, 3927-3937 (1990).
31. S. Burnett, J. Moreno-Lopez & U. Pettersson, Messenger RNAs from the E1 region of bovine papillomavirus type 1 detected in virus-infected bovine cells, Nucleic Acids Res. 15, 8607-8620 (1987).
32. S. Sun, L. Thorner, M. Lentz, P. MacPherson & M. Botchan, Identification of a 68-kilodalton nuclear ATPbinding phosphoprotein encoded by bovine papillomavirus type 1, J.Virol. 64, 5093-5105 (1990). (Pubitemid 20329832)
33. W. G. Hubert & P. F. Lambert, The 23-kilodalton E1 phosphoprotein of bovine papillomavirus type 1 is nonessential for stable plasmid replication in murine C127 cells, J.Virol. 67, 2932-2937 (1993). (Pubitemid 23118897)
34. S. Barksdale & C. C. Baker, Differentiation-specific alternative splicing of bovine papillomavirus late mRNAs, J.Virol. 69, 6553-6556 (1995).
35. K. Neary, B. H. Horwitz & D. DiMaio, Mutational analysis of open reading frame E4 of bovine papillomavirus type 1, J.Virol. 61, 1248-1252 (1987). (Pubitemid 17044041)
36. D. L. Black, Mechanisms of alternative pre-messenger RNA splicing, Annu.Rev.Biochem. 72, 291-336 (2003). (Pubitemid 36930448)
37. S. F. Jamison & M. A. Garcia-Blanco, An ATPindependent U2 small nuclear ribonucleoprotein particle/precursor mRNA complex requires both splice sites and the polypyrimidine tract, Proc.Natl.Acad.Sci.U.S.A 89, 5482-5486 (1992).
38. S. Michaud & R. Reed, An ATP-independent complex commits pre-mRNA to the mammalian spliceosome assembly pathway, Genes Dev. 5, 2534-2546 (1991). (Pubitemid 21905937)
39. B. Ruskin, P. D. Zamore & M. R. Green, A factor, U2AF, is required for U2 snRNP binding and splicing complex assembly, Cell 52, 207-219 (1988). (Pubitemid 18042857)
40. D. Staknis & R. Reed, Direct interactions between premRNA and six U2 small nuclear ribonucleoproteins during spliceosome assembly, Mol.Cell Biol. 14, 2994-3005 (1994). (Pubitemid 24132713)
41. P. D. Zamore & M. R. Green, Identification, purification, and biochemical characterization of U2 small nuclear ribonucleoprotein auxiliary factor, Proc.Natl.Acad.Sci.U.S.A 86, 9243-9247 (1989). (Pubitemid 20010401)
42. R. Das, Z. Zhou & R. Reed, Functional association of U2 snRNP with the ATP-independent spliceosomal complex E, Mol.Cell 5, 779-787 (2000).
43. A. Watakabe, K. Tanaka & Y. Shimura, The role of exon sequences in splice site selection, Genes Dev. 7, 407- 418 (1993). (Pubitemid 23139234)
44. Z. M. Zheng, Regulation of alternative RNA splicing by exon definition and exon sequences in viral and mammalian gene expression, J.Biomed.Sci. 11, 278-294 (2004).
45. Z. M. Zheng, P. He & C. C. Baker, Selection of the bovine papillomavirus type 1 nucleotide 3225 3' splice site is regulated through an exonic splicing enhancer and its juxtaposed exonic splicing suppressor, J.Virol. 70, 4691- 4699 (1996). (Pubitemid 26187463)
46. Z. M. Zheng, P. J. He & C. C. Baker, Structural, functional, and protein binding analyses of bovine papillomavirus type 1 exonic splicing enhancers, J.Virol. 71, 9096-9107 (1997). (Pubitemid 27492349)
47. Z. M. Zheng, M. Huynen & C. C. Baker, A pyrimidinerich exonic splicing suppressor binds multiple RNA splicing factors and inhibits spliceosome assembly, Proc.Natl.Acad.Sci.U.S.A 95, 14088-14093 (1998). (Pubitemid 28549325)
48. Z. M. Zheng, P. J. He & C. C. Baker, Function of a bovine papillomavirus type 1 exonic splicing suppressor requires a suboptimal upstream 3' splice site, J.Virol. 73, 29-36 (1999). (Pubitemid 28565342)
49. Z. M. Zheng, E. S. Reid & C. C. Baker, Utilization of the bovine papillomavirus type 1 late-stage-specific nucleotide 3605 3' splice site is modulated by a novel exonic bipartite regulator but not by an intronic purine-rich element, J.Virol. 74, 10612-10622 (2000).
50. X. Liu, A. Mayeda, M. Tao & Z. M. Zheng, Exonic splicing enhancer-dependent selection of the bovine papillomavirus type 1 nucleotide 3225 3' splice site can be rescued in a cell lacking splicing factor ASF/SF2 through activation of the phosphatidylinositol 3- kinase/Akt pathway, J.Virol. 77, 2105-2115 (2003). (Pubitemid 36110023)
51. M. G. McPhillips, T. Veerapraditsin, S. A. Cumming, D. Karali, S. G. Milligan, W. Boner, I. M. Morgan & S. V. Graham, SF2/ASF binds the human papillomavirus type 16 late RNA control element and is regulated during differentiation of virus-infected epithelial cells, J.Virol. 78, 10598-10605 (2004). (Pubitemid 39258386)
52. K. Ryan, O. Calvo & J. L. Manley, Evidence that polyadenylation factor CPSF-73 is the mRNA 3' processing endonuclease, RNA 10, 565-573 (2004). (Pubitemid 38405934)
53. C. R. Mandel, S. Kaneko, H. Zhang, D. Gebauer, V. Vethantham, J. L. Manley & L. Tong, Polyadenylation factor CPSF-73 is the pre-mRNA 3'-end-processing endonuclease, Nature 444, 953-956 (2006). (Pubitemid 46025011)
54. G. M. Gilmartin, Eukaryotic mRNA 3' processing: a common means to different ends, Genes Dev. 19, 2517- 2521 (2005). (Pubitemid 41565970)
55. D. A. Mangus, M. C. Evans & A. Jacobson, Poly (A)- transcriptional control of gene expression, Genome Biol. 4, 223 (2003).
56. J. A. Chekanova & D. A. Belostotsky, Evidence that poly (A) binding protein has an evolutionarily conserved function in facilitating mRNA biogenesis and export, RNA 9, 1476-1490 (2003). (Pubitemid 37463474)
57. E. M. Andrews & D. DiMaio, Hierarchy of polyadenylation site usage by bovine papillomavirus in transformed mouse cells, J.Virol. 67, 7705-7710 (1993). (Pubitemid 23343910)
58. C. C. Baker & J. S. Noe, Transcriptional termination between bovine papillomavirus type 1 (BPV-1) early and late polyadenylation sites blocks late transcription in BPV- 1-transformed cells, J.Virol. 63, 3529-3534 (1989). (Pubitemid 19181418)
59. P. A. Furth & C. C. Baker, An element in the bovine papillomavirus late 3' untranslated region reduces polyadenylated cytoplasmic RNA levels, J.Virol. 65, 5806- 5812 (1991).
60. M. D. Koffa, S. V. Graham, Y. Takagaki, J. L. Manley & J. B. Clements, The human papillomavirus type 16 negative regulatory RNA element interacts with three proteins that act at different posttranscriptional levels, Proc.Natl.Acad.Sci.U.S.A 97, 4677-4682 (2000). (Pubitemid 30238617)
61. S. A. Cumming, C. E. Repellin, M. McPhillips, J. C. Radford, J. B. Clements & S. V. Graham, The human papillomavirus type 31 late 3' untranslated region contains a complex bipartite negative regulatory element, J.Virol. 76, 5993-6003 (2002). (Pubitemid 34556294)
62. P. A. Furth, W. T. Choe, J. H. Rex, J. C. Byrne & C. C. Baker, Sequences homologous to 5' splice sites are required for the inhibitory activity of papillomavirus late 3' untranslated regions, Mol.Cell Biol. 14, 5278-5289 (1994).
63. S. Vagner, U. Ruegsegger, S. I. Gunderson, W. Keller & I. W. Mattaj, Position-dependent inhibition of the cleavage step of pre-mRNA 3'-end processing by U1 snRNP, RNA 6, 178-188 (2000). (Pubitemid 30091589)
64. S. I. Gunderson, M. Polycarpou-Schwarz & I. W. Mattaj, U1 snRNP inhibits pre-mRNA polyadenylation through a direct interaction between U1 70K and poly (A) polymerase, Mol.Cell 1, 255-264 (1998). (Pubitemid 128378666)
65. W. C. Boelens, E. J. Jansen, W. J. van Venrooij, R. Stripecke, I. W. Mattaj & S. I. Gunderson, The human U1 snRNP-specific U1A protein inhibits polyadenylation of its own pre-mRNA, Cell 72, 881-892 (1993). (Pubitemid 23110230)
66. J. Ma, S. I. Gunderson & C. Phillips, Non-snRNP U1A levels decrease during mammalian B-cell differentiation and release the IgM secretory poly (A) site from repression, RNA 12, 122-132 (2006). (Pubitemid 43037460)
67. N. J. Proudfoot, A. Furger & M. J. Dye, Integrating mRNA processing with transcription, Cell 108, 501-512 (2002). (Pubitemid 34260875)
68. R. Reed & H. Cheng, TREX, SR proteins and export of mRNA, Curr.Opin.Cell Biol. 17, 269-273 (2005). (Pubitemid 40719916)
69. H. H. Le, D. Gatfield, E. Izaurralde & M. J. Moore, The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsensemediated mRNA decay, EMBO J. 20, 4987-4997 (2001). (Pubitemid 32848650)
70. M. E. Stroupe, T. O. Tange, D. R. Thomas, M. J. Moore & N. Grigorieff, The three-dimensional arcitecture of the EJC core, J.Mol.Biol. 360, 743-749 (2006). (Pubitemid 43993920)
71. D. Gatfield, H. H. Le, C. Schmitt, I. C. Braun, T. Kocher, M. Wilm & E. Izaurralde, The DExH/D box protein HEL/UAP56 is essential for mRNA nuclear export in Drosophila, Curr.Biol. 11, 1716-1721 (2001). (Pubitemid 33037786)
72. T. H. Jensen, J. Boulay, M. Rosbash & D. Libri, The DECD box putative ATPase Sub2p is an early mRNA export factor, Curr.Biol. 11, 1711-1715 (2001). (Pubitemid 33037785)
73. D. Longman, I. L. Johnstone & J. F. Caceres, The Ref/Aly proteins are dispensable for mRNA export and development in Caenorhabditis elegans, RNA 9, 881-891 (2003). (Pubitemid 36734785)
74. M. MacMorris, C. Brocker & T. Blumenthal, UAP56 levels affect viability and mRNA export in Caenorhabditis elegans, RNA. 9, 847-857 (2003). (Pubitemid 36734782)
75. M. L. Luo, Z. Zhou, K. Magni, C. Christoforides, J. Rappsilber, M. Mann & R. Reed, Pre-mRNA splicing and mRNA export linked by direct interactions between UAP56 and Aly, Nature 413, 644-647 (2001). (Pubitemid 32964065)
76. I. C. Braun, A. Herold, M. Rode, E. Conti & E. Izaurralde, Overexpression of TAP/p15 heterodimers bypasses nuclear retention and stimulates nuclear mRNA export, J.Biol.Chem. 276, 20536-20543 (2001).
77. Y. Huang & J. A. Steitz, Splicing factors SRp20 and 9G8 promote the nucleocytoplasmic export of mRNA, Mol.Cell 7, 899-905 (2001). (Pubitemid 32436449)
78. Y. Huang, R. Gattoni, J. Stevenin & J. A. Steitz, SR splicing factors serve as adapter proteins for TAPdependent mRNA export, Mol.Cell 11, 837-843 (2003). (Pubitemid 36385134)
79. Y. Huang, T. A. Yario & J. A. Steitz, A molecular link between SR protein dephosphorylation and mRNA export, Proc.Natl.Acad.Sci.U.S.A 101, 9666-9670 (2004). (Pubitemid 38869293)
80. Y. Hargous, G. M. Hautbergue, A. M. Tintaru, L. Skrisovska, A. P. Golovanov, J. Stevenin, L. Y. Lian, S. A. Wilson & F. H. Allain, Molecular basis of RNA recognition and TAP binding by the SR proteins SRp20 and 9G8, EMBO J. 25, 5126-5137 (2006). (Pubitemid 44658530)
81. O. Danos, M. Katinka & M. Yaniv, Human papillomavirus 1a complete DNA sequence: a novel type of genome organization among papovaviridae, EMBO J. 1, 231-236 (1982).
82. I. Dvoretzky, R. Shober, S. K. Chattopadhyay & D. R. Lowy, A quantitative in vitro focus assay for bovine papilloma virus, Virology 103, 369-375 (1980). (Pubitemid 10119863)
83. C. C. Baker & C. Calef, Maps of papillomavirus mRNA transcripts, in "The human papillomaviruses compendium" (Los Alamos National Laboratory, Ed.), Los Alamos National Laboratory, (1995).
84. K. Middleton, W. Peh, S. Southern, H. Griffin, K. Sotlar, T. Nakahara, A. El Sherif, L. Morris, R. Seth, M. Hibma, D. Jenkins, P. Lambert, N. Coleman & J. Doorbar, Organization of human papillomavirus productive cycle during neoplastic progression provides a basis for selection of diagnostic markers, J.Virol. 77, 10186-10201 (2003). (Pubitemid 37129663)