Skip to main content
NCBI home page
Molecular and Cellular Biology logoLink to Molecular and Cellular Biology
. 1987 Feb;7(2):864–874. doi: 10.1128/mcb.7.2.864

Adenovirus origin of DNA replication: sequence requirements for replication in vitro.

R J Wides, M D Challberg, D R Rawlins, T J Kelly
PMCID: PMC365145  PMID: 3821730

Abstract

The initiation of adenovirus DNA takes place at the termini of the viral genome and requires the presence of specific nucleotide sequence elements. To define the sequence organization of the viral origin, we tested a large number of deletion, insertion, and base substitution mutants for their ability to support initiation and replication in vitro. The data demonstrate that the origin consists of at least three functionally distinct domains, A, B, and C. Domain A (nucleotides 1 to 18) contains the minimal sequence sufficient for origin function. Domains B (nucleotides 19 to 40) and C (nucleotides 41 to 51) contain accessory sequences that significantly increase the activity of the minimal origin. The presence of domain B increases the efficiency of initiation by more than 10-fold in vitro, and the presence of domains B and C increases the efficiency of initiation by more than 30-fold. Mutations that alter the distance between the minimal origin and the accessory domains by one or two base pairs dramatically decrease initiation efficiency. This critical spacing requirement suggests that there are specific interactions between the factors that recognize the two regions.

Full text

PDF
864

Images in this article

868Image
on p.868
869Image
on p.869
870Image
on p.870
872Image
on p.872

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Adhya S., Shneidman P. S., Hurwitz J. Reconstruction of adenovirus replication origins with a human nuclear factor I binding site. J Biol Chem. 1986 Mar 5;261(7):3339–3346. [PubMed] [Google Scholar]
  2. Arrand J. R., Roberts R. J. The nucleotide sequences at the termini of adenovirus-2 DNA. J Mol Biol. 1979 Mar 15;128(4):577–594. doi: 10.1016/0022-2836(79)90294-8. [DOI] [PubMed] [Google Scholar]
  3. BURTON K. A study of the conditions and mechanism of the diphenylamine reaction for the colorimetric estimation of deoxyribonucleic acid. Biochem J. 1956 Feb;62(2):315–323. doi: 10.1042/bj0620315. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Baker T. A., Sekimizu K., Funnell B. E., Kornberg A. Extensive unwinding of the plasmid template during staged enzymatic initiation of DNA replication from the origin of the Escherichia coli chromosome. Cell. 1986 Apr 11;45(1):53–64. doi: 10.1016/0092-8674(86)90537-4. [DOI] [PubMed] [Google Scholar]
  5. Barany F. Two-codon insertion mutagenesis of plasmid genes by using single-stranded hexameric oligonucleotides. Proc Natl Acad Sci U S A. 1985 Jun;82(12):4202–4206. doi: 10.1073/pnas.82.12.4202. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Challberg M. D., Desiderio S. V., Kelly T. J., Jr Adenovirus DNA replication in vitro: characterization of a protein covalently linked to nascent DNA strands. Proc Natl Acad Sci U S A. 1980 Sep;77(9):5105–5109. doi: 10.1073/pnas.77.9.5105. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Challberg M. D., Kelly T. J., Jr Adenovirus DNA replication in vitro. Proc Natl Acad Sci U S A. 1979 Feb;76(2):655–659. doi: 10.1073/pnas.76.2.655. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Challberg M. D., Kelly T. J., Jr Adenovirus DNA replication in vitro: origin and direction of daughter strand synthesis. J Mol Biol. 1979 Dec 25;135(4):999–1012. doi: 10.1016/0022-2836(79)90524-2. [DOI] [PubMed] [Google Scholar]
  9. Challberg M. D., Ostrove J. M., Kelly T. J., Jr Initiation of adenovirus DNA replication: detection of covalent complexes between nucleotide and the 80-kilodalton terminal protein. J Virol. 1982 Jan;41(1):265–270. doi: 10.1128/jvi.41.1.265-270.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Challberg M. D., Rawlins D. R. Template requirements for the initiation of adenovirus DNA replication. Proc Natl Acad Sci U S A. 1984 Jan;81(1):100–104. doi: 10.1073/pnas.81.1.100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Chen E. Y., Seeburg P. H. Supercoil sequencing: a fast and simple method for sequencing plasmid DNA. DNA. 1985 Apr;4(2):165–170. doi: 10.1089/dna.1985.4.165. [DOI] [PubMed] [Google Scholar]
  12. Desiderio S. V., Kelly T. J., Jr Structure of the linkage between adenovirus DNA and the 55,000 molecular weight terminal protein. J Mol Biol. 1981 Jan 15;145(2):319–337. doi: 10.1016/0022-2836(81)90208-4. [DOI] [PubMed] [Google Scholar]
  13. Ellens D. J., Sussenbach J. S., Jansz H. S. Studies on the mechanism of replication of adenovirus DNA. III. Electron microscopy of replicating DNA. Virology. 1974 Oct;61(2):427–442. doi: 10.1016/0042-6822(74)90279-7. [DOI] [PubMed] [Google Scholar]
  14. Enomoto T., Lichy J. H., Ikeda J. E., Hurwitz J. Adenovirus DNA replication in vitro: purification of the terminal protein in a functional form. Proc Natl Acad Sci U S A. 1981 Nov;78(11):6779–6783. doi: 10.1073/pnas.78.11.6779. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Friefeld B. R., Lichy J. H., Hurwitz J., Horwitz M. S. Evidence for an altered adenovirus DNA polymerase in cells infected with the mutant H5ts149. Proc Natl Acad Sci U S A. 1983 Mar;80(6):1589–1593. doi: 10.1073/pnas.80.6.1589. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Green M., Symington J., Brackmann K. H., Cartas M. A., Thornton H., Young L. Immunological and chemical identification of intracellular forms of adenovirus type 2 terminal protein. J Virol. 1981 Nov;40(2):541–550. doi: 10.1128/jvi.40.2.541-550.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Gronostajski R. M., Adhya S., Nagata K., Guggenheimer R. A., Hurwitz J. Site-specific DNA binding of nuclear factor I: analyses of cellular binding sites. Mol Cell Biol. 1985 May;5(5):964–971. doi: 10.1128/mcb.5.5.964. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Guggenheimer R. A., Stillman B. W., Nagata K., Tamanoi F., Hurwitz J. DNA sequences required for the in vitro replication of adenovirus DNA. Proc Natl Acad Sci U S A. 1984 May;81(10):3069–3073. doi: 10.1073/pnas.81.10.3069. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Guo L. H., Wu R. New rapid methods for DNA sequencing based in exonuclease III digestion followed by repair synthesis. Nucleic Acids Res. 1982 Mar 25;10(6):2065–2084. doi: 10.1093/nar/10.6.2065. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Hanahan D. Studies on transformation of Escherichia coli with plasmids. J Mol Biol. 1983 Jun 5;166(4):557–580. doi: 10.1016/s0022-2836(83)80284-8. [DOI] [PubMed] [Google Scholar]
  21. Hay R. T. The origin of adenovirus DNA replication: minimal DNA sequence requirement in vivo. EMBO J. 1985 Feb;4(2):421–426. doi: 10.1002/j.1460-2075.1985.tb03645.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Hennighausen L., Siebenlist U., Danner D., Leder P., Rawlins D., Rosenfeld P., Kelly T., Jr High-affinity binding site for a specific nuclear protein in the human IgM gene. Nature. 1985 Mar 21;314(6008):289–292. doi: 10.1038/314289a0. [DOI] [PubMed] [Google Scholar]
  23. Laemmli U. K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970 Aug 15;227(5259):680–685. doi: 10.1038/227680a0. [DOI] [PubMed] [Google Scholar]
  24. Lally C., Dörper T., Gröger W., Antoine G., Winnacker E. L. A size analysis of the adenovirus replicon. EMBO J. 1984 Feb;3(2):333–337. doi: 10.1002/j.1460-2075.1984.tb01807.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Lechner R. L., Kelly T. J., Jr The structure of replicating adenovirus 2 DNA molecules. Cell. 1977 Dec;12(4):1007–1020. doi: 10.1016/0092-8674(77)90165-9. [DOI] [PubMed] [Google Scholar]
  26. Leegwater P. A., van Driel W., van der Vliet P. C. Recognition site of nuclear factor I, a sequence-specific DNA-binding protein from HeLa cells that stimulates adenovirus DNA replication. EMBO J. 1985 Jun;4(6):1515–1521. doi: 10.1002/j.1460-2075.1985.tb03811.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Lichy J. H., Field J., Horwitz M. S., Hurwitz J. Separation of the adenovirus terminal protein precursor from its associated DNA polymerase: role of both proteins in the initiation of adenovirus DNA replication. Proc Natl Acad Sci U S A. 1982 Sep;79(17):5225–5229. doi: 10.1073/pnas.79.17.5225. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Lichy J. H., Horwitz M. S., Hurwitz J. Formation of a covalent complex between the 80,000-dalton adenovirus terminal protein and 5'-dCMP in vitro. Proc Natl Acad Sci U S A. 1981 May;78(5):2678–2682. doi: 10.1073/pnas.78.5.2678. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Nagata K., Guggenheimer R. A., Enomoto T., Lichy J. H., Hurwitz J. Adenovirus DNA replication in vitro: identification of a host factor that stimulates synthesis of the preterminal protein-dCMP complex. Proc Natl Acad Sci U S A. 1982 Nov;79(21):6438–6442. doi: 10.1073/pnas.79.21.6438. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Nagata K., Guggenheimer R. A., Hurwitz J. Specific binding of a cellular DNA replication protein to the origin of replication of adenovirus DNA. Proc Natl Acad Sci U S A. 1983 Oct;80(20):6177–6181. doi: 10.1073/pnas.80.20.6177. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Norris K., Norris F., Christiansen L., Fiil N. Efficient site-directed mutagenesis by simultaneous use of two primers. Nucleic Acids Res. 1983 Aug 11;11(15):5103–5112. doi: 10.1093/nar/11.15.5103. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Ostrove J. M., Rosenfeld P., Williams J., Kelly T. J., Jr In vitro complementation as an assay for purification of adenovirus DNA replication proteins. Proc Natl Acad Sci U S A. 1983 Feb;80(4):935–939. doi: 10.1073/pnas.80.4.935. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Pincus S., Robertson W., Rekosh D. Characterization of the effect of aphidicolin on adenovirus DNA replication: evidence in support of a protein primer model of initiation. Nucleic Acids Res. 1981 Oct 10;9(19):4919–4938. doi: 10.1093/nar/9.19.4919. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Rawlins D. R., Rosenfeld P. J., Wides R. J., Challberg M. D., Kelly T. J., Jr Structure and function of the adenovirus origin of replication. Cell. 1984 May;37(1):309–319. doi: 10.1016/0092-8674(84)90327-1. [DOI] [PubMed] [Google Scholar]
  35. Rijnders A. W., van Bergen B. G., van der Vliet P. C., Sussenbach J. S. Specific binding of the adenovirus terminal protein precursor-DNA polymerase complex to the origin of DNA replication. Nucleic Acids Res. 1983 Dec 20;11(24):8777–8789. doi: 10.1093/nar/11.24.8777. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Rosenfeld P. J., Kelly T. J. Purification of nuclear factor I by DNA recognition site affinity chromatography. J Biol Chem. 1986 Jan 25;261(3):1398–1408. [PubMed] [Google Scholar]
  37. Rosenfeld P. J., O'Neill E. A., Wides R. J., Kelly T. J. Sequence-specific interactions between cellular DNA-binding proteins and the adenovirus origin of DNA replication. Mol Cell Biol. 1987 Feb;7(2):875–886. doi: 10.1128/mcb.7.2.875. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Shortle D., Nathans D. Local mutagenesis: a method for generating viral mutants with base substitutions in preselected regions of the viral genome. Proc Natl Acad Sci U S A. 1978 May;75(5):2170–2174. doi: 10.1073/pnas.75.5.2170. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Stillman B. W., Lewis J. B., Chow L. T., Mathews M. B., Smart J. E. Identification of the gene and mRNA for the adenovirus terminal protein precursor. Cell. 1981 Feb;23(2):497–508. doi: 10.1016/0092-8674(81)90145-8. [DOI] [PubMed] [Google Scholar]
  40. Tamanoi F., Stillman B. W. Function of adenovirus terminal protein in the initiation of DNA replication. Proc Natl Acad Sci U S A. 1982 Apr;79(7):2221–2225. doi: 10.1073/pnas.79.7.2221. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Tamanoi F., Stillman B. W. Initiation of adenovirus DNA replication in vitro requires a specific DNA sequence. Proc Natl Acad Sci U S A. 1983 Nov;80(21):6446–6450. doi: 10.1073/pnas.80.21.6446. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Vieira J., Messing J. The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers. Gene. 1982 Oct;19(3):259–268. doi: 10.1016/0378-1119(82)90015-4. [DOI] [PubMed] [Google Scholar]
  43. Wang K., Pearson G. D. Adenovirus sequences required for replication in vivo. Nucleic Acids Res. 1985 Jul 25;13(14):5173–5187. doi: 10.1093/nar/13.14.5173. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Zoller M. J., Smith M. Oligonucleotide-directed mutagenesis of DNA fragments cloned into M13 vectors. Methods Enzymol. 1983;100:468–500. doi: 10.1016/0076-6879(83)00074-9. [DOI] [PubMed] [Google Scholar]
  45. Zoller M. J., Smith M. Oligonucleotide-directed mutagenesis: a simple method using two oligonucleotide primers and a single-stranded DNA template. DNA. 1984 Dec;3(6):479–488. doi: 10.1089/dna.1.1984.3.479. [DOI] [PubMed] [Google Scholar]
  46. de Vries E., van Driel W., Tromp M., van Boom J., van der Vliet P. C. Adenovirus DNA replication in vitro: site-directed mutagenesis of the nuclear factor I binding site of the Ad2 origin. Nucleic Acids Res. 1985 Jul 11;13(13):4935–4952. doi: 10.1093/nar/13.13.4935. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. van Bergen B. G., van der Ley P. A., van Driel W., van Mansfeld A. D., van der Vliet P. C. Replication of origin containing adenovirus DNA fragments that do not carry the terminal protein. Nucleic Acids Res. 1983 Apr 11;11(7):1975–1989. doi: 10.1093/nar/11.7.1975. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. van der Vliet P. C., Levine A. J. DNA-binding proteins specific for cells infected by adenovirus. Nat New Biol. 1973 Dec 12;246(154):170–174. doi: 10.1038/newbio246170a0. [DOI] [PubMed] [Google Scholar]

Articles from Molecular and Cellular Biology are provided here courtesy of Taylor & Francis

RESOURCES