A cellular homolog of hepatitis delta antigen: Implications for viral replication and evolution

Science

Volumn 274, Issue 5284, 1996, Pages 90-94

  Brazas, Robert ^a   Ganem, Don ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENE PRODUCT; TRANSCRIPTION FACTOR;

AMINO ACID SEQUENCE; ARTICLE; DELTA AGENT HEPATITIS; DNA SEQUENCE; EVOLUTION; GENOME; OPEN READING FRAME; PRIORITY JOURNAL; REGULATORY MECHANISM; RNA GENE; RNA STRUCTURE; RNA SYNTHESIS; SEQUENCE ANALYSIS; VIROID; VIRUS REPLICATION;

AMINO ACID SEQUENCE; CARRIER PROTEINS; CELL LINE; CLONING, MOLECULAR; EVOLUTION; GENOME, VIRAL; HEPATITIS ANTIGENS; HEPATITIS DELTA ANTIGENS; HEPATITIS DELTA VIRUS; HUMANS; LIVER; MOLECULAR SEQUENCE DATA; RNA, MESSENGER; RNA, VIRAL; SEQUENCE ALIGNMENT; TRANSFECTION; TUMOR CELLS, CULTURED; VIROIDS; VIRUS REPLICATION;

DELTA VIRUS; HEPATITIS DELTA VIRUS; VIROIDS;

EID: 0029763579     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.274.5284.90     Document Type: Article

References (47)

1. M. Rizzetto, Hepatology 3, 729 (1983).
2. A. Smedile, M. Rizetto, J. Gerin, Prog. Liver Dis. 12, 157 (1994); M. Rizzetto et al., Proc. Natl. Acad. Sci. U.S.A. 77, 6124 (1980).
3. A. Smedile, M. Rizetto, J. Gerin, Prog. Liver Dis. 12, 157 (1994); M. Rizzetto et al., Proc. Natl. Acad. Sci. U.S.A. 77, 6124 (1980).
4. K. S. Wang et al., Nature 323, 508 (1986); A. Kos, R. Kijkema, A. Arnberg, P. van der Meide, H. Schellekens, ibid., p. 558; P. J. Chen et al., Proc. Natl. Acad. Sci. U.S.A. 83, 8774 (1986); S. Makino et al., Nature 329, 343 (1987).
5. K. S. Wang et al., Nature 323, 508 (1986); A. Kos, R. Kijkema, A. Arnberg, P. van der Meide, H. Schellekens, ibid., p. 558; P. J. Chen et al., Proc. Natl. Acad. Sci. U.S.A. 83, 8774 (1986); S. Makino et al., Nature 329, 343 (1987).
6. K. S. Wang et al., Nature 323, 508 (1986); A. Kos, R. Kijkema, A. Arnberg, P. van der Meide, H. Schellekens, ibid., p. 558; P. J. Chen et al., Proc. Natl. Acad. Sci. U.S.A. 83, 8774 (1986); S. Makino et al., Nature 329, 343 (1987).
7. K. S. Wang et al., Nature 323, 508 (1986); A. Kos, R. Kijkema, A. Arnberg, P. van der Meide, H. Schellekens, ibid., p. 558; P. J. Chen et al., Proc. Natl. Acad. Sci. U.S.A. 83, 8774 (1986); S. Makino et al., Nature 329, 343 (1987).
8. Y. P. Xia, C.-T. Yeh, J.-H. Ou, M. Lai, J. Virol. 66, 914 (1992); M.-F. Chang, S. Chang, C.-I. Chang, K. Wu, H.-Y. Kang, ibid., p. 6019; S. Hwang, C. Lee, M. Lai, Virology 190, 413 (1992).
9. Y. P. Xia, C.-T. Yeh, J.-H. Ou, M. Lai, J. Virol. 66, 914 (1992); M.-F. Chang, S. Chang, C.-I. Chang, K. Wu, H.-Y. Kang, ibid., p. 6019; S. Hwang, C. Lee, M. Lai, Virology 190, 413 (1992).
10. Y. P. Xia, C.-T. Yeh, J.-H. Ou, M. Lai, J. Virol. 66, 914 (1992); M.-F. Chang, S. Chang, C.-I. Chang, K. Wu, H.-Y. Kang, ibid., p. 6019; S. Hwang, C. Lee, M. Lai, Virology 190, 413 (1992).
11. J.-H. Lin, M.-F. Chang, S. Baker, S. Govindarajan, M. Lai, J. Virol. 64, 4051 (1990); M. Chao, S.-Y. Hsieh, J. Taylor, ibid. 65, 4057 (1991).
12. J.-H. Lin, M.-F. Chang, S. Baker, S. Govindarajan, M. Lai, J. Virol. 64, 4051 (1990); M. Chao, S.-Y. Hsieh, J. Taylor, ibid. 65, 4057 (1991).
13. M. Kuo, M. Chao, J. Taylor, ibid. 63, 1945 (1989); J. Glenn, J. Taylor, J. White, ibid. 64, 3104 (1990).
14. M. Kuo, M. Chao, J. Taylor, ibid. 63, 1945 (1989); J. Glenn, J. Taylor, J. White, ibid. 64, 3104 (1990).
15. R. Symons, Semin. Virol. 1, 75 (1990).
16. G. A. Prody, J. T. Bakos, J. M. Buzayan, I. R. Schneider, G. Breuning, Science 231, 1577 (1986); A. Forster and R. Symons, Cell 50, 9 (1987).
17. G. A. Prody, J. T. Bakos, J. M. Buzayan, I. R. Schneider, G. Breuning, Science 231, 1577 (1986); A. Forster and R. Symons, Cell 50, 9 (1987).
18. H.-N. Wu and M. M. C. Lai, Science 243, 652 (1989); L. Sharmeen, M. Kuo, G. Dinter-Gottlieb, J. Taylor, J. Virol. 62, 2674 (1988); H.-N. Wu and M. Lai, Mol. Cell. Biol. 10, 5575 (1990); M. Kuo, L. Sharmeen, G. Dinter-Gottlieb, J. Taylor, J. Virol 62, 4439 (1988); L. Sharmeen. M. Kuo, J. Taylor, ibid. 63, 1428 (1989).
19. H.-N. Wu and M. M. C. Lai, Science 243, 652 (1989); L. Sharmeen, M. Kuo, G. Dinter-Gottlieb, J. Taylor, J. Virol. 62, 2674 (1988); H.-N. Wu and M. Lai, Mol. Cell. Biol. 10, 5575 (1990); M. Kuo, L. Sharmeen, G. Dinter-Gottlieb, J. Taylor, J. Virol 62, 4439 (1988); L. Sharmeen. M. Kuo, J. Taylor, ibid. 63, 1428 (1989).
20. H.-N. Wu and M. M. C. Lai, Science 243, 652 (1989); L. Sharmeen, M. Kuo, G. Dinter-Gottlieb, J. Taylor, J. Virol. 62, 2674 (1988); H.-N. Wu and M. Lai, Mol. Cell. Biol. 10, 5575 (1990); M. Kuo, L. Sharmeen, G. Dinter-Gottlieb, J. Taylor, J. Virol 62, 4439 (1988); L. Sharmeen. M. Kuo, J. Taylor, ibid. 63, 1428 (1989).
21. H.-N. Wu and M. M. C. Lai, Science 243, 652 (1989); L. Sharmeen, M. Kuo, G. Dinter-Gottlieb, J. Taylor, J. Virol. 62, 2674 (1988); H.-N. Wu and M. Lai, Mol. Cell. Biol. 10, 5575 (1990); M. Kuo, L. Sharmeen, G. Dinter-Gottlieb, J. Taylor, J. Virol 62, 4439 (1988); L. Sharmeen. M. Kuo, J. Taylor, ibid. 63, 1428 (1989).
22. H.-N. Wu and M. M. C. Lai, Science 243, 652 (1989); L. Sharmeen, M. Kuo, G. Dinter-Gottlieb, J. Taylor, J. Virol. 62, 2674 (1988); H.-N. Wu and M. Lai, Mol. Cell. Biol. 10, 5575 (1990); M. Kuo, L. Sharmeen, G. Dinter-Gottlieb, J. Taylor, J. Virol 62, 4439 (1988); L. Sharmeen. M. Kuo, J. Taylor, ibid. 63, 1428 (1989).
23. A. D. Branch and H. D. Robertson, Science 223, 450 (1984).
24. T. MacNaughton, E. Gowans, S. McNamara, C. Burrell, Virology 184, 387 (1991); T.-B. Fu and J. Taylor, J. Virol. 67, 6965 (1993).
25. T. MacNaughton, E. Gowans, S. McNamara, C. Burrell, Virology 184, 387 (1991); T.-B. Fu and J. Taylor, J. Virol. 67, 6965 (1993).
26. + colonies were isolated, and, after rescreening and checking for specificity, 12 isolates were identified as true positives. The 12 clones were subjected to restriction mapping and shown to contain three classes of inserts. DNA sequencing revealed that the three classes (DIPA-2, -17, and -7) contained cDNAs that were derived from the same mRNA and differed only in their 5′ and 3′ ends.
27. + colonies were isolated, and, after rescreening and checking for specificity, 12 isolates were identified as true positives. The 12 clones were subjected to restriction mapping and shown to contain three classes of inserts. DNA sequencing revealed that the three classes (DIPA-2, -17, and -7) contained cDNAs that were derived from the same mRNA and differed only in their 5′ and 3′ ends.
28. +] RNA was then purified from total RNA with Oligotex-dT (Qiagen). RNA samples were fractionated in a standard 1% agarose-formaldehyde gel, transferred to a positively charged nylon membrane (Boehringer Mannheim) under mild alkaline conditions, and fixed to the membrane as described [R. Low and T. Rausch, Biotechniques 17, 1026 (1994)]. The human multiple-tissue Northern (RNA) blot was obtained from Clontech. The digoxigenin-labeled DIPA-specific (DIPA nucleotides 443 to 212) and actin-specific [from pTRI-β-actin template (Ambion)] riboprobes were synthesized with the use of a MEGAscript kit (Ambion) in combination with the digoxigenin RNA labeling mix (Boehringer Mannheim). The blots were prehybridized and hybridized essentially as described by Low and Rausch. After hybridization, the blots were washed (15 min per wash) at 72°C with solutions comprising 0.1% SDS and 2X, 0.5X, and 0.1X standard saline citrate, respectively, and the hybridized digoxigenin-labeled probes were detected essentially as described [G. Engle-Blum et al., Anal. Biochem. 210, 235 (1993)]. Exposures times varied between 1 and 60 min depending on the experiment.
29. +] RNA was then purified from total RNA with Oligotex-dT (Qiagen). RNA samples were fractionated in a standard 1% agarose-formaldehyde gel, transferred to a positively charged nylon membrane (Boehringer Mannheim) under mild alkaline conditions, and fixed to the membrane as described [R. Low and T. Rausch, Biotechniques 17, 1026 (1994)]. The human multiple-tissue Northern (RNA) blot was obtained from Clontech. The digoxigenin-labeled DIPA-specific (DIPA nucleotides 443 to 212) and actin-specific [from pTRI-β-actin template (Ambion)] riboprobes were synthesized with the use of a MEGAscript kit (Ambion) in combination with the digoxigenin RNA labeling mix (Boehringer Mannheim). The blots were prehybridized and hybridized essentially as described by Low and Rausch. After hybridization, the blots were washed (15 min per wash) at 72°C with solutions comprising 0.1% SDS and 2X, 0.5X, and 0.1X standard saline citrate, respectively, and the hybridized digoxigenin-labeled probes were detected essentially as described [G. Engle-Blum et al., Anal. Biochem. 210, 235 (1993)]. Exposures times varied between 1 and 60 min depending on the experiment.
30. + RNA isolated from 293T cells with the use of Oligotex-dT. The DIPA 5′-end cDNA product generated was T-A cloned into pBluescript II KS+ (Stratagene) as described [F. M. Ausubel et al., Eds., Current Protocols in Molecular Biology (Wiley, Brooklyn, NY, 1994), vol. 2]. Three different clones were sequenced, and all three contained the same cDNA insert, which corresponded to a perfect extension of the 5′ end of the DIPA-2 clone by an additional 150 base pairs (bp). This 5′ cDNA product was combined with the DIPA-2 cDNA isolate with the use of a common Not I restriction site, generating the full-length DIPA cDNA clone. The complete DIPA cDNA was resequenced with the use of deoxyinosine triphosphate in the preserce of 10% (v/v) dimethylsulfoxide as described [P. Winship. Nucleic Acids Res. 17, 1266 (1989); D. DeShazer, G. E. Wood, R. L. Friedman, Biotechniques 17, 288 (1994)]. The full-length DIPA cDNA comprised 879 bp, excluding the poly(A) tail. The AUG start codon of the open reading frame begins at nucleotide 29, and the last base of the UGA stop codon is at nucleotide 637. The sequence of the DIPA cDNA has been deposited in GenBank with the accession number U63825.
31. + RNA isolated from 293T cells with the use of Oligotex-dT. The DIPA 5′-end cDNA product generated was T-A cloned into pBluescript II KS+ (Stratagene) as described [F. M. Ausubel et al., Eds., Current Protocols in Molecular Biology (Wiley, Brooklyn, NY, 1994), vol. 2]. Three different clones were sequenced, and all three contained the same cDNA insert, which corresponded to a perfect extension of the 5′ end of the DIPA-2 clone by an additional 150 base pairs (bp). This 5′ cDNA product was combined with the DIPA-2 cDNA isolate with the use of a common Not I restriction site, generating the full-length DIPA cDNA clone. The complete DIPA cDNA was resequenced with the use of deoxyinosine triphosphate in the preserce of 10% (v/v) dimethylsulfoxide as described [P. Winship. Nucleic Acids Res. 17, 1266 (1989); D. DeShazer, G. E. Wood, R. L. Friedman, Biotechniques 17, 288 (1994)]. The full-length DIPA cDNA comprised 879 bp, excluding the poly(A) tail. The AUG start codon of the open reading frame begins at nucleotide 29, and the last base of the UGA stop codon is at nucleotide 637. The sequence of the DIPA cDNA has been deposited in GenBank with the accession number U63825.
32. + RNA isolated from 293T cells with the use of Oligotex-dT. The DIPA 5′-end cDNA product generated was T-A cloned into pBluescript II KS+ (Stratagene) as described [F. M. Ausubel et al., Eds., Current Protocols in Molecular Biology (Wiley, Brooklyn, NY, 1994), vol. 2]. Three different clones were sequenced, and all three contained the same cDNA insert, which corresponded to a perfect extension of the 5′ end of the DIPA-2 clone by an additional 150 base pairs (bp). This 5′ cDNA product was combined with the DIPA-2 cDNA isolate with the use of a common Not I restriction site, generating the full-length DIPA cDNA clone. The complete DIPA cDNA was resequenced with the use of deoxyinosine triphosphate in the preserce of 10% (v/v) dimethylsulfoxide as described [P. Winship. Nucleic Acids Res. 17, 1266 (1989); D. DeShazer, G. E. Wood, R. L. Friedman, Biotechniques 17, 288 (1994)]. The full-length DIPA cDNA comprised 879 bp, excluding the poly(A) tail. The AUG start codon of the open reading frame begins at nucleotide 29, and the last base of the UGA stop codon is at nucleotide 637. The sequence of the DIPA cDNA has been deposited in GenBank with the accession number U63825.
33. + RNA isolated from 293T cells with the use of Oligotex-dT. The DIPA 5′-end cDNA product generated was T-A cloned into pBluescript II KS+ (Stratagene) as described [F. M. Ausubel et al., Eds., Current Protocols in Molecular Biology (Wiley, Brooklyn, NY, 1994), vol. 2]. Three different clones were sequenced, and all three contained the same cDNA insert, which corresponded to a perfect extension of the 5′ end of the DIPA-2 clone by an additional 150 base pairs (bp). This 5′ cDNA product was combined with the DIPA-2 cDNA isolate with the use of a common Not I restriction site, generating the full-length DIPA cDNA clone. The complete DIPA cDNA was resequenced with the use of deoxyinosine triphosphate in the preserce of 10% (v/v) dimethylsulfoxide as described [P. Winship. Nucleic Acids Res. 17, 1266 (1989); D. DeShazer, G. E. Wood, R. L. Friedman, Biotechniques 17, 288 (1994)]. The full-length DIPA cDNA comprised 879 bp, excluding the poly(A) tail. The AUG start codon of the open reading frame begins at nucleotide 29, and the last base of the UGA stop codon is at nucleotide 637. The sequence of the DIPA cDNA has been deposited in GenBank with the accession number U63825.
34. R. Brazas and D. Ganem, data not shown.
35. J. Polo et al., J. Virol 69, 4880 (1995).
36. D. W. Lazinski and J. M. Taylor, ibid. 67, 2672 (1993).
37. P.-J. Chen et al., ibid. 66, 2853 (1992); Y. Xia and M. Lai, ibid., p. 6641.
38. P.-J. Chen et al., ibid. 66, 2853 (1992); Y. Xia and M. Lai, ibid., p. 6641.
39. C. Lee, J. Lin, M. Chao, K. McKnight, M. Lai, ibid. 67, 2221 (1993).
40. Preliminary alignments with the use of the BLAST algorithm [S. F. Altschul, W. Gish, W. Miller, E. W. Myers, D. J. Lipman, J. Mol. Biol. 215. 403 (1990)] identified three small regions of homology between DIPA and members of the FRA (FOS-related antigen) transcription factor family [D. R. Cohen and T. Curran, Mol. Cell. Biol. 8, 2063 (1988)]. The homology is limited to the bZIP DNA binding and dimerization domain of the FRA proteins and includes both predicted coiled-coil regions of DIPA. The sequence identity between DIPA and rat FRA1 is 35% over the FRA1 bZIP domain.
41. Preliminary alignments with the use of the BLAST algorithm [S. F. Altschul, W. Gish, W. Miller, E. W. Myers, D. J. Lipman, J. Mol. Biol. 215. 403 (1990)] identified three small regions of homology between DIPA and members of the FRA (FOS-related antigen) transcription factor family [D. R. Cohen and T. Curran, Mol. Cell. Biol. 8, 2063 (1988)]. The homology is limited to the bZIP DNA binding and dimerization domain of the FRA proteins and includes both predicted coiled-coil regions of DIPA. The sequence identity between DIPA and rat FRA1 is 35% over the FRA1 bZIP domain.
42. In all figures, pCMV is the new name given to pCEP4 (Invitrogen). The entire HDAg open reading frame was cloned into pCEP4, thereby creating pCMV-HDAg, in which expression of HDAg is under the control of the cytomegalovirus promoter. The pCMV-HDAg ccΔ and ARMΔ expression vectors were constructed by subcloning the mutant HDAg open reading frames from pDL448 and pDL501 (16) into pCEP4. The HA epitope tag sequence was cloned as a double-stranded oligonucteotide into the Nco I site present in the DIPA cDNA at the native ATG start codon, and the HA-DIPA fusion cDNA was then cloned into pCEP4, thereby creating the expression vector pCMV-HA-DIPA. The coiled-coil mutant m1 and m2 DIPA open reading frames were created by the insertion of a BgI II site between codons 67 and 68 and an Sph I site between codons 127 and 128, respectively, with the use of site-directed mutagenesis (Altered Sites II; Promega). 293T cells were transfected by calcium phosphate precipitation [C. Chen and H. Okayama, Mol. Cell. Biol. 7, 2745 (1987)] with the combinations of plasmids (5 μg of each plasmid) shown in Fig. 3. Two days after transfection, the cells were plated in 10-cm plates containing medium supplemented with hygromycin (200 μg/ml) (Boehringer Mannheim). At∼80 to 90% confluence, cells from each plate were harvested and lysed in a solution containing 50 mM tris-HCl (pH 7.5), 400 mM NaCl, 0.2% NP-40, and protease inhibitors. The lysate was adjusted to 100 mM NaCl with buffer lacking NaCl and centrifuged at 100,000g for 60 min. The resulting supernatant was subjected to immunoprecipitation as described [E. Harlow and D. Lane, Antibodies: A Laboratory Manual (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1988)] with monoclonal antibodies (12CA5) to HA. Both lysate supernatants and immunoprecipitates were fractionated by SDS-polyacrylamide gel electrophoresis on 12.5 or 15% (for HDAg deletion derivatives) gels, and the resolved proteins were transferred to Immobilon-P (Millipore) membranes and subjected to immunoblot analysis with either polyclonal antibodies to DIPA (1 : 4000 dilution) (CalTag) or polyclonal antibodies to HDAg (1 : 15,000 dilution) (CalTag). Immune complexes were detected with horseradish peroxidase-conjugated goat antibodies to rabbit immunoglobulin G (1 : 7500 dilution) (Gibco BRL) and enhanced chemiluminescence (ECL; Amersham).
43. In all figures, pCMV is the new name given to pCEP4 (Invitrogen). The entire HDAg open reading frame was cloned into pCEP4, thereby creating pCMV-HDAg, in which expression of HDAg is under the control of the cytomegalovirus promoter. The pCMV-HDAg ccΔ and ARMΔ expression vectors were constructed by subcloning the mutant HDAg open reading frames from pDL448 and pDL501 (16) into pCEP4. The HA epitope tag sequence was cloned as a double-stranded oligonucteotide into the Nco I site present in the DIPA cDNA at the native ATG start codon, and the HA-DIPA fusion cDNA was then cloned into pCEP4, thereby creating the expression vector pCMV-HA-DIPA. The coiled-coil mutant m1 and m2 DIPA open reading frames were created by the insertion of a BgI II site between codons 67 and 68 and an Sph I site between codons 127 and 128, respectively, with the use of site-directed mutagenesis (Altered Sites II; Promega). 293T cells were transfected by calcium phosphate precipitation [C. Chen and H. Okayama, Mol. Cell. Biol. 7, 2745 (1987)] with the combinations of plasmids (5 μg of each plasmid) shown in Fig. 3. Two days after transfection, the cells were plated in 10-cm plates containing medium supplemented with hygromycin (200 μg/ml) (Boehringer Mannheim). At∼80 to 90% confluence, cells from each plate were harvested and lysed in a solution containing 50 mM tris-HCl (pH 7.5), 400 mM NaCl, 0.2% NP-40, and protease inhibitors. The lysate was adjusted to 100 mM NaCl with buffer lacking NaCl and centrifuged at 100,000g for 60 min. The resulting supernatant was subjected to immunoprecipitation as described [E. Harlow and D. Lane, Antibodies: A Laboratory Manual (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1988)] with monoclonal antibodies (12CA5) to HA. Both lysate supernatants and immunoprecipitates were fractionated by SDS-polyacrylamide gel electrophoresis on 12.5 or 15% (for HDAg deletion derivatives) gels, and the resolved proteins were transferred to Immobilon-P (Millipore) membranes and subjected to immunoblot analysis with either polyclonal antibodies to DIPA (1 : 4000 dilution) (CalTag) or polyclonal antibodies to HDAg (1 : 15,000 dilution) (CalTag). Immune complexes were detected with horseradish peroxidase-conjugated goat antibodies to rabbit immunoglobulin G (1 : 7500 dilution) (Gibco BRL) and enhanced chemiluminescence (ECL; Amersham).
44. A. D. Branch et al., Science 243, 649 (1989).
45. D. M. Engelman, T. A. Steitz, A. Goldman, Annu. Rev. Biophys. Biophys. Chem. 15, 321 (1986).
46. A. Lupas, Methods Enzymol. 266, 513 (1996).
47. Supported by Howard Hughes Medical Institute.