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. 1995 Oct;69(10):6131–6139. doi: 10.1128/jvi.69.10.6131-6139.1995

Vaccinia virus gene A18R encodes an essential DNA helicase.

D A Simpson 1, R C Condit 1
PMCID: PMC189510  PMID: 7545242

Abstract

The vaccinia virus A18R protein is a DNA-dependent ATPase that contains the canonical sequence motifs associated with the DEXH group of DNA and RNA helicases. Investigation of A18R protein function during infection indicated it functions in the early and late phases of vaccinia virus transcription. The A18R protein shares sequence similarity with the mammalian DNA helicase ERCC3. The ERCC3 protein has a dual function: it is a component of the transcription factor TFIIH and is an essential participant in the cellular nucleotide excision repair pathway. Here we present evidence that the A18R protein is a DNA helicase that unwinds duplex DNA in a 3'-to-5' direction. The A18R helicase was inactive on RNA-DNA and RNA-RNA hybrids. The A18R unwinding activity was most efficient on DNA substrates with lengths of 20 nucleotides or less, and its unwinding activity was not stimulated by the addition of Escherichia coli single-strand-binding protein (SSB), the bacteriophage T4 gene 32 SSB, or the vaccinia virus I3L protein, a putative SSB. We have used an electrophoretic gel mobility shift assay to show that the A18R protein forms a stable complex with single-stranded DNA, and to a lesser extent RNA, in a reaction that does not require ATP.

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Selected References

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  1. Baldick C. J., Jr, Cassetti M. C., Harris N., Moss B. Ordered assembly of a functional preinitiation transcription complex, containing vaccinia virus early transcription factor and RNA polymerase, on an immobilized template. J Virol. 1994 Sep;68(9):6052–6056. doi: 10.1128/jvi.68.9.6052-6056.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Baldick C. J., Jr, Keck J. G., Moss B. Mutational analysis of the core, spacer, and initiator regions of vaccinia virus intermediate-class promoters. J Virol. 1992 Aug;66(8):4710–4719. doi: 10.1128/jvi.66.8.4710-4719.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Baldick C. J., Jr, Moss B. Characterization and temporal regulation of mRNAs encoded by vaccinia virus intermediate-stage genes. J Virol. 1993 Jun;67(6):3515–3527. doi: 10.1128/jvi.67.6.3515-3527.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bayliss C. D., Condit R. C. Temperature-sensitive mutants in the vaccinia virus A18R gene increase double-stranded RNA synthesis as a result of aberrant viral transcription. Virology. 1993 May;194(1):254–262. doi: 10.1006/viro.1993.1256. [DOI] [PubMed] [Google Scholar]
  5. Bayliss C. D., Condit R. C. The vaccinia virus A18R gene product is a DNA-dependent ATPase. J Biol Chem. 1995 Jan 27;270(4):1550–1556. doi: 10.1074/jbc.270.4.1550. [DOI] [PubMed] [Google Scholar]
  6. Broyles S. S., Moss B. Homology between RNA polymerases of poxviruses, prokaryotes, and eukaryotes: nucleotide sequence and transcriptional analysis of vaccinia virus genes encoding 147-kDa and 22-kDa subunits. Proc Natl Acad Sci U S A. 1986 May;83(10):3141–3145. doi: 10.1073/pnas.83.10.3141. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Buratowski S. DNA repair and transcription: the helicase connection. Science. 1993 Apr 2;260(5104):37–38. doi: 10.1126/science.8465198. [DOI] [PubMed] [Google Scholar]
  8. Cohrs R. J., Condit R. C., Pacha R. F., Thompson C. L., Sharma O. K. Modulation of ppp(A2'p)nA-dependent RNase by a temperature-sensitive mutant of vaccinia virus. J Virol. 1989 Feb;63(2):948–951. doi: 10.1128/jvi.63.2.948-951.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Condit R. C., Motyczka A. Isolation and preliminary characterization of temperature-sensitive mutants of vaccinia virus. Virology. 1981 Aug;113(1):224–241. doi: 10.1016/0042-6822(81)90150-1. [DOI] [PubMed] [Google Scholar]
  10. Condit R. C., Motyczka A., Spizz G. Isolation, characterization, and physical mapping of temperature-sensitive mutants of vaccinia virus. Virology. 1983 Jul 30;128(2):429–443. doi: 10.1016/0042-6822(83)90268-4. [DOI] [PubMed] [Google Scholar]
  11. Condit R. C., Niles E. G. Orthopoxvirus genetics. Curr Top Microbiol Immunol. 1990;163:1–39. doi: 10.1007/978-3-642-75605-4_1. [DOI] [PubMed] [Google Scholar]
  12. Crute J. J., Mocarski E. S., Lehman I. R. A DNA helicase induced by herpes simplex virus type 1. Nucleic Acids Res. 1988 Jul 25;16(14A):6585–6596. doi: 10.1093/nar/16.14.6585. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Davison A. J., Moss B. Structure of vaccinia virus early promoters. J Mol Biol. 1989 Dec 20;210(4):749–769. doi: 10.1016/0022-2836(89)90107-1. [DOI] [PubMed] [Google Scholar]
  14. Davison A. J., Moss B. Structure of vaccinia virus late promoters. J Mol Biol. 1989 Dec 20;210(4):771–784. doi: 10.1016/0022-2836(89)90108-3. [DOI] [PubMed] [Google Scholar]
  15. Drapkin R., Reardon J. T., Ansari A., Huang J. C., Zawel L., Ahn K., Sancar A., Reinberg D. Dual role of TFIIH in DNA excision repair and in transcription by RNA polymerase II. Nature. 1994 Apr 21;368(6473):769–772. doi: 10.1038/368769a0. [DOI] [PubMed] [Google Scholar]
  16. Feaver W. J., Svejstrup J. Q., Bardwell L., Bardwell A. J., Buratowski S., Gulyas K. D., Donahue T. F., Friedberg E. C., Kornberg R. D. Dual roles of a multiprotein complex from S. cerevisiae in transcription and DNA repair. Cell. 1993 Dec 31;75(7):1379–1387. doi: 10.1016/0092-8674(93)90624-y. [DOI] [PubMed] [Google Scholar]
  17. Fuerst T. R., Niles E. G., Studier F. W., Moss B. Eukaryotic transient-expression system based on recombinant vaccinia virus that synthesizes bacteriophage T7 RNA polymerase. Proc Natl Acad Sci U S A. 1986 Nov;83(21):8122–8126. doi: 10.1073/pnas.83.21.8122. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Goodrich J. A., Tjian R. Transcription factors IIE and IIH and ATP hydrolysis direct promoter clearance by RNA polymerase II. Cell. 1994 Apr 8;77(1):145–156. doi: 10.1016/0092-8674(94)90242-9. [DOI] [PubMed] [Google Scholar]
  19. Gorbalenya A. E., Koonin E. V., Donchenko A. P., Blinov V. M. Two related superfamilies of putative helicases involved in replication, recombination, repair and expression of DNA and RNA genomes. Nucleic Acids Res. 1989 Jun 26;17(12):4713–4730. doi: 10.1093/nar/17.12.4713. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Gulyas K. D., Donahue T. F. SSL2, a suppressor of a stem-loop mutation in the HIS4 leader encodes the yeast homolog of human ERCC-3. Cell. 1992 Jun 12;69(6):1031–1042. doi: 10.1016/0092-8674(92)90621-i. [DOI] [PubMed] [Google Scholar]
  21. Guzder S. N., Sung P., Bailly V., Prakash L., Prakash S. RAD25 is a DNA helicase required for DNA repair and RNA polymerase II transcription. Nature. 1994 Jun 16;369(6481):578–581. doi: 10.1038/369578a0. [DOI] [PubMed] [Google Scholar]
  22. Hagler J., Luo Y., Shuman S. Factor-dependent transcription termination by vaccinia RNA polymerase. Kinetic coupling and requirement for ATP hydrolysis. J Biol Chem. 1994 Apr 1;269(13):10050–10060. [PubMed] [Google Scholar]
  23. Hanawalt P. C. Transcription-coupled repair and human disease. Science. 1994 Dec 23;266(5193):1957–1958. doi: 10.1126/science.7801121. [DOI] [PubMed] [Google Scholar]
  24. Harosh I., Naumovski L., Friedberg E. C. Purification and characterization of Rad3 ATPase/DNA helicase from Saccharomyces cerevisiae. J Biol Chem. 1989 Dec 5;264(34):20532–20539. [PubMed] [Google Scholar]
  25. Johnson G. P., Goebel S. J., Paoletti E. An update on the vaccinia virus genome. Virology. 1993 Oct;196(2):381–401. doi: 10.1006/viro.1993.1494. [DOI] [PubMed] [Google Scholar]
  26. Kerr S. M., Johnston L. H., Odell M., Duncan S. A., Law K. M., Smith G. L. Vaccinia DNA ligase complements Saccharomyces cerevisiae cdc9, localizes in cytoplasmic factories and affects virulence and virus sensitivity to DNA damaging agents. EMBO J. 1991 Dec;10(13):4343–4350. doi: 10.1002/j.1460-2075.1991.tb05012.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Klein B., Filon A. R., van Zeeland A. A., van der Eb A. J. Survival of UV-irradiated vaccinia virus in normal and xeroderma pigmentosum fibroblasts; evidence for repair of UV-damaged viral DNA. Mutat Res. 1994 May 1;307(1):25–32. doi: 10.1016/0027-5107(94)90274-7. [DOI] [PubMed] [Google Scholar]
  28. Koonin E. V., Senkevich T. G. Vaccinia virus encodes four putative DNA and/or RNA helicases distantly related to each other. J Gen Virol. 1992 Apr;73(Pt 4):989–993. doi: 10.1099/0022-1317-73-4-989. [DOI] [PubMed] [Google Scholar]
  29. Kovacs G. R., Rosales R., Keck J. G., Moss B. Modification of the cascade model for regulation of vaccinia virus gene expression: purification of a prereplicative, late-stage-specific transcription factor. J Virol. 1994 May;68(5):3443–3447. doi: 10.1128/jvi.68.5.3443-3447.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Lanzetta P. A., Alvarez L. J., Reinach P. S., Candia O. A. An improved assay for nanomole amounts of inorganic phosphate. Anal Biochem. 1979 Nov 15;100(1):95–97. doi: 10.1016/0003-2697(79)90115-5. [DOI] [PubMed] [Google Scholar]
  31. Lee C. G., Hurwitz J. A new RNA helicase isolated from HeLa cells that catalytically translocates in the 3' to 5' direction. J Biol Chem. 1992 Mar 5;267(7):4398–4407. [PubMed] [Google Scholar]
  32. Lohman T. M. Helicase-catalyzed DNA unwinding. J Biol Chem. 1993 Feb 5;268(4):2269–2272. [PubMed] [Google Scholar]
  33. Luo Y., Hagler J., Shuman S. Discrete functional stages of vaccinia virus early transcription during a single round of RNA synthesis in vitro. J Biol Chem. 1991 Jul 15;266(20):13303–13310. [PubMed] [Google Scholar]
  34. Ma L., Siemssen E. D., Noteborn H. M., van der Eb A. J. The xeroderma pigmentosum group B protein ERCC3 produced in the baculovirus system exhibits DNA helicase activity. Nucleic Acids Res. 1994 Oct 11;22(20):4095–4102. doi: 10.1093/nar/22.20.4095. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Matson S. W., Kaiser-Rogers K. A. DNA helicases. Annu Rev Biochem. 1990;59:289–329. doi: 10.1146/annurev.bi.59.070190.001445. [DOI] [PubMed] [Google Scholar]
  36. Moss B. Regulation of vaccinia virus transcription. Annu Rev Biochem. 1990;59:661–688. doi: 10.1146/annurev.bi.59.070190.003305. [DOI] [PubMed] [Google Scholar]
  37. Moyer R. W. The role of the host cell nucleus in vaccinia virus morphogenesis. Virus Res. 1987 Sep;8(3):173–191. doi: 10.1016/0168-1702(87)90014-1. [DOI] [PubMed] [Google Scholar]
  38. Pacha R. F., Condit R. C. Characterization of a temperature-sensitive mutant of vaccinia virus reveals a novel function that prevents virus-induced breakdown of RNA. J Virol. 1985 Nov;56(2):395–403. doi: 10.1128/jvi.56.2.395-403.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Pacha R. F., Meis R. J., Condit R. C. Structure and expression of the vaccinia virus gene which prevents virus-induced breakdown of RNA. J Virol. 1990 Aug;64(8):3853–3863. doi: 10.1128/jvi.64.8.3853-3863.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Parvin J. D., Sharp P. A. DNA topology and a minimal set of basal factors for transcription by RNA polymerase II. Cell. 1993 May 7;73(3):533–540. doi: 10.1016/0092-8674(93)90140-l. [DOI] [PubMed] [Google Scholar]
  41. Qiu H., Park E., Prakash L., Prakash S. The Saccharomyces cerevisiae DNA repair gene RAD25 is required for transcription by RNA polymerase II. Genes Dev. 1993 Nov;7(11):2161–2171. doi: 10.1101/gad.7.11.2161. [DOI] [PubMed] [Google Scholar]
  42. Rosales R., Harris N., Ahn B. Y., Moss B. Purification and identification of a vaccinia virus-encoded intermediate stage promoter-specific transcription factor that has homology to eukaryotic transcription factor SII (TFIIS) and an additional role as a viral RNA polymerase subunit. J Biol Chem. 1994 May 13;269(19):14260–14267. [PubMed] [Google Scholar]
  43. Rosales R., Sutter G., Moss B. A cellular factor is required for transcription of vaccinia viral intermediate-stage genes. Proc Natl Acad Sci U S A. 1994 Apr 26;91(9):3794–3798. doi: 10.1073/pnas.91.9.3794. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Sancar A. Mechanisms of DNA excision repair. Science. 1994 Dec 23;266(5193):1954–1956. doi: 10.1126/science.7801120. [DOI] [PubMed] [Google Scholar]
  45. Schaeffer L., Roy R., Humbert S., Moncollin V., Vermeulen W., Hoeijmakers J. H., Chambon P., Egly J. M. DNA repair helicase: a component of BTF2 (TFIIH) basic transcription factor. Science. 1993 Apr 2;260(5104):58–63. doi: 10.1126/science.8465201. [DOI] [PubMed] [Google Scholar]
  46. Schwer B., Stunnenberg H. G. Vaccinia virus late transcripts generated in vitro have a poly(A) head. EMBO J. 1988 Apr;7(4):1183–1190. doi: 10.1002/j.1460-2075.1988.tb02929.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Selby C. P., Sancar A. Molecular mechanism of transcription-repair coupling. Science. 1993 Apr 2;260(5104):53–58. doi: 10.1126/science.8465200. [DOI] [PubMed] [Google Scholar]
  48. Seo Y. S., Hurwitz J. Isolation of helicase alpha, a DNA helicase from HeLa cells stimulated by a fork structure and signal-stranded DNA-binding proteins. J Biol Chem. 1993 May 15;268(14):10282–10295. [PubMed] [Google Scholar]
  49. Seo Y. S., Lee S. H., Hurwitz J. Isolation of a DNA helicase from HeLa cells requiring the multisubunit human single-stranded DNA-binding protein for activity. J Biol Chem. 1991 Jul 15;266(20):13161–13170. [PubMed] [Google Scholar]
  50. Shuman S. Vaccinia virus RNA helicase. Directionality and substrate specificity. J Biol Chem. 1993 Jun 5;268(16):11798–11802. [PubMed] [Google Scholar]
  51. Shuman S. Vaccinia virus RNA helicase: an essential enzyme related to the DE-H family of RNA-dependent NTPases. Proc Natl Acad Sci U S A. 1992 Nov 15;89(22):10935–10939. doi: 10.1073/pnas.89.22.10935. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. Simpson D. A., Condit R. C. The vaccinia virus A18R protein plays a role in viral transcription during both the early and the late phases of infection. J Virol. 1994 Jun;68(6):3642–3649. doi: 10.1128/jvi.68.6.3642-3649.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Stuart D. T., Upton C., Higman M. A., Niles E. G., McFadden G. A poxvirus-encoded uracil DNA glycosylase is essential for virus viability. J Virol. 1993 May;67(5):2503–2512. doi: 10.1128/jvi.67.5.2503-2512.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Svejstrup J. Q., Wang Z., Feaver W. J., Wu X., Bushnell D. A., Donahue T. F., Friedberg E. C., Kornberg R. D. Different forms of TFIIH for transcription and DNA repair: holo-TFIIH and a nucleotide excision repairosome. Cell. 1995 Jan 13;80(1):21–28. doi: 10.1016/0092-8674(95)90447-6. [DOI] [PubMed] [Google Scholar]
  55. Sweder K. S., Hanawalt P. C. The COOH terminus of suppressor of stem loop (SSL2/RAD25) in yeast is essential for overall genomic excision repair and transcription-coupled repair. J Biol Chem. 1994 Jan 21;269(3):1852–1857. [PubMed] [Google Scholar]
  56. Traktman P. The enzymology of poxvirus DNA replication. Curr Top Microbiol Immunol. 1990;163:93–123. doi: 10.1007/978-3-642-75605-4_4. [DOI] [PubMed] [Google Scholar]
  57. Vos J. C., Sasker M., Stunnenberg H. G. Vaccinia virus capping enzyme is a transcription initiation factor. EMBO J. 1991 Sep;10(9):2553–2558. doi: 10.1002/j.1460-2075.1991.tb07795.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. Wang Z., Svejstrup J. Q., Feaver W. J., Wu X., Kornberg R. D., Friedberg E. C. Transcription factor b (TFIIH) is required during nucleotide-excision repair in yeast. Nature. 1994 Mar 3;368(6466):74–76. doi: 10.1038/368074a0. [DOI] [PubMed] [Google Scholar]
  59. Wright C. F., Coroneos A. M. Purification of the late transcription system of vaccinia virus: identification of a novel transcription factor. J Virol. 1993 Dec;67(12):7264–7270. doi: 10.1128/jvi.67.12.7264-7270.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  60. van Vuuren A. J., Vermeulen W., Ma L., Weeda G., Appeldoorn E., Jaspers N. G., van der Eb A. J., Bootsma D., Hoeijmakers J. H., Humbert S. Correction of xeroderma pigmentosum repair defect by basal transcription factor BTF2 (TFIIH). EMBO J. 1994 Apr 1;13(7):1645–1653. doi: 10.1002/j.1460-2075.1994.tb06428.x. [DOI] [PMC free article] [PubMed] [Google Scholar]

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