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. 1994 Jul;68(7):4377–4383. doi: 10.1128/jvi.68.7.4377-4383.1994

Excision of DNA fragments corresponding to the unit-length a sequence of herpes simplex virus type 1 and terminus variation predominate on one side of the excised fragment.

K Umene 1
PMCID: PMC236361  PMID: 8207811

Abstract

DNA fragments corresponding to the unit-length a sequence of herpes simplex virus type 1 (HSV-1) were identified in HSV-1 DNA preparations extracted by the method of Hirt. The DNA fragments were molecularly cloned, and nucleotide sequences were determined. Most termini of the fragments were at sites on DR1 corresponding to the termini of linear HSV-1 DNA generated by the cleavage-packaging system. In one-step growth experiments, DNA fragments of the unit-length a sequence appeared simultaneously with the termini of linear HSV-1 DNAs produced by cleavage of circular and concatemeric DNAs. Therefore, excision of the unit-length a sequence appeared closely related to the cleavage-packaging system. Termini of the excised DNA fragments of the variant a sequence with two DR2 arrays varied on the L-component side, while termini on the S-component side were at the site on DR1 corresponding to the authentic cleavage site. It is thus assumed that the cleavage-packaging system functions adequately on the DR1 second distal from the S component, and cleavages of other DR1 are rare and less accurate. If this notion is tenable, then most termini on the S-component side of the excised DNA fragments are derived from the second DR1 properly cleaved and should be constant, while termini on the L-component side are from regions on and around the DR1 third distal from the S component and may be variable. Cleavage of DR1 is likely to be affected by the topological relationship with the S component.

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Selected References

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

  1. Bortner C., Hernandez T. R., Lehman I. R., Griffith J. Herpes simplex virus 1 single-strand DNA-binding protein (ICP8) will promote homologous pairing and strand transfer. J Mol Biol. 1993 May 20;231(2):241–250. doi: 10.1006/jmbi.1993.1279. [DOI] [PubMed] [Google Scholar]
  2. Brown S. M., Subak-Sharpe J. H., Harland J., MacLean A. R. Analysis of intrastrain recombination in herpes simplex virus type 1 strain 17 and herpes simplex virus type 2 strain HG52 using restriction endonuclease sites as unselected markers and temperature-sensitive lesions as selected markers. J Gen Virol. 1992 Feb;73(Pt 2):293–301. doi: 10.1099/0022-1317-73-2-293. [DOI] [PubMed] [Google Scholar]
  3. Bruckner R. C., Dutch R. E., Zemelman B. V., Mocarski E. S., Lehman I. R. Recombination in vitro between herpes simplex virus type 1 a sequences. Proc Natl Acad Sci U S A. 1992 Nov 15;89(22):10950–10954. doi: 10.1073/pnas.89.22.10950. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Chou J., Roizman B. Characterization of DNA sequence-common and sequence-specific proteins binding to cis-acting sites for cleavage of the terminal a sequence of the herpes simplex virus 1 genome. J Virol. 1989 Mar;63(3):1059–1068. doi: 10.1128/jvi.63.3.1059-1068.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Chou J., Roizman B. Isomerization of herpes simplex virus 1 genome: identification of the cis-acting and recombination sites within the domain of the a sequence. Cell. 1985 Jul;41(3):803–811. doi: 10.1016/s0092-8674(85)80061-1. [DOI] [PubMed] [Google Scholar]
  6. Chou J., Roizman B. The terminal a sequence of the herpes simplex virus genome contains the promoter of a gene located in the repeat sequences of the L component. J Virol. 1986 Feb;57(2):629–637. doi: 10.1128/jvi.57.2.629-637.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Davison A. J., Wilkie N. M. Nucleotide sequences of the joint between the L and S segments of herpes simplex virus types 1 and 2. J Gen Virol. 1981 Aug;55(Pt 2):315–331. doi: 10.1099/0022-1317-55-2-315. [DOI] [PubMed] [Google Scholar]
  8. Deiss L. P., Chou J., Frenkel N. Functional domains within the a sequence involved in the cleavage-packaging of herpes simplex virus DNA. J Virol. 1986 Sep;59(3):605–618. doi: 10.1128/jvi.59.3.605-618.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Desai P., DeLuca N. A., Glorioso J. C., Person S. Mutations in herpes simplex virus type 1 genes encoding VP5 and VP23 abrogate capsid formation and cleavage of replicated DNA. J Virol. 1993 Mar;67(3):1357–1364. doi: 10.1128/jvi.67.3.1357-1364.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Dutch R. E., Bruckner R. C., Mocarski E. S., Lehman I. R. Herpes simplex virus type 1 recombination: role of DNA replication and viral a sequences. J Virol. 1992 Jan;66(1):277–285. doi: 10.1128/jvi.66.1.277-285.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Jones D., Isfort R., Witter R., Kost R., Kung H. J. Retroviral insertions into a herpesvirus are clustered at the junctions of the short repeat and short unique sequences. Proc Natl Acad Sci U S A. 1993 May 1;90(9):3855–3859. doi: 10.1073/pnas.90.9.3855. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Kobayashi I. Mechanisms for gene conversion and homologous recombination: the double-strand break repair model and the successive half crossing-over model. Adv Biophys. 1992;28:81–133. doi: 10.1016/0065-227x(92)90023-k. [DOI] [PubMed] [Google Scholar]
  13. MacLean A. R., ul-Fareed M., Robertson L., Harland J., Brown S. M. Herpes simplex virus type 1 deletion variants 1714 and 1716 pinpoint neurovirulence-related sequences in Glasgow strain 17+ between immediate early gene 1 and the 'a' sequence. J Gen Virol. 1991 Mar;72(Pt 3):631–639. doi: 10.1099/0022-1317-72-3-631. [DOI] [PubMed] [Google Scholar]
  14. Mocarski E. S., Deiss L. P., Frenkel N. Nucleotide sequence and structural features of a novel US-a junction present in a defective herpes simplex virus genome. J Virol. 1985 Jul;55(1):140–146. doi: 10.1128/jvi.55.1.140-146.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Mocarski E. S., Roizman B. Site-specific inversion sequence of the herpes simplex virus genome: domain and structural features. Proc Natl Acad Sci U S A. 1981 Nov;78(11):7047–7051. doi: 10.1073/pnas.78.11.7047. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Mocarski E. S., Roizman B. Structure and role of the herpes simplex virus DNA termini in inversion, circularization and generation of virion DNA. Cell. 1982 Nov;31(1):89–97. doi: 10.1016/0092-8674(82)90408-1. [DOI] [PubMed] [Google Scholar]
  17. Nasseri M., Mocarski E. S. The cleavage recognition signal is contained within sequences surrounding an a-a junction in herpes simplex virus DNA. Virology. 1988 Nov;167(1):25–30. doi: 10.1016/0042-6822(88)90050-5. [DOI] [PubMed] [Google Scholar]
  18. Pater M. M., Hyman R. W., Rapp F. Isolation of herpes simplex virus DNA from the "hirt supernatant". Virology. 1976 Dec;75(2):481–483. doi: 10.1016/0042-6822(76)90046-5. [DOI] [PubMed] [Google Scholar]
  19. Roizman B. The structure and isomerization of herpes simplex virus genomes. Cell. 1979 Mar;16(3):481–494. doi: 10.1016/0092-8674(79)90023-0. [DOI] [PubMed] [Google Scholar]
  20. Smiley J. R., Duncan J., Howes M. Sequence requirements for DNA rearrangements induced by the terminal repeat of herpes simplex virus type 1 KOS DNA. J Virol. 1990 Oct;64(10):5036–5050. doi: 10.1128/jvi.64.10.5036-5050.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Smiley J. R., Lavery C., Howes M. The herpes simplex virus type 1 (HSV-1) a sequence serves as a cleavage/packaging signal but does not drive recombinational genome isomerization when it is inserted into the HSV-2 genome. J Virol. 1992 Dec;66(12):7505–7510. doi: 10.1128/jvi.66.12.7505-7510.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Szostak J. W., Orr-Weaver T. L., Rothstein R. J., Stahl F. W. The double-strand-break repair model for recombination. Cell. 1983 May;33(1):25–35. doi: 10.1016/0092-8674(83)90331-8. [DOI] [PubMed] [Google Scholar]
  23. Taha M. Y., Clements G. B., Brown S. M. The herpes simplex virus type 2 (HG52) variant JH2604 has a 1488 bp deletion which eliminates neurovirulence in mice. J Gen Virol. 1989 Nov;70(Pt 11):3073–3078. doi: 10.1099/0022-1317-70-11-3073. [DOI] [PubMed] [Google Scholar]
  24. Tengelsen L. A., Pederson N. E., Shaver P. R., Wathen M. W., Homa F. L. Herpes simplex virus type 1 DNA cleavage and encapsidation require the product of the UL28 gene: isolation and characterization of two UL28 deletion mutants. J Virol. 1993 Jun;67(6):3470–3480. doi: 10.1128/jvi.67.6.3470-3480.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Umene K. Conversion of a fraction of the unique sequence to part of the inverted repeats in the S component of the herpes simplex virus type 1 genome. J Gen Virol. 1986 Jun;67(Pt 6):1035–1048. doi: 10.1099/0022-1317-67-6-1035. [DOI] [PubMed] [Google Scholar]
  26. Umene K., Enquist L. W. Isolation of novel herpes simplex virus type 1 derivatives with tandem duplications of DNA sequences encoding immediate-early mRNA-5 and an origin of replication. J Virol. 1985 Feb;53(2):607–615. doi: 10.1128/jvi.53.2.607-615.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Umene K. Herpes simplex virus type 1 variant a sequence generated by recombination and breakage of the a sequence in defined regions, including the one involved in recombination. J Virol. 1993 Sep;67(9):5685–5691. doi: 10.1128/jvi.67.9.5685-5691.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Umene K. Intermolecular recombination of the herpes simplex virus type 1 genome analysed using two strains differing in restriction enzyme cleavage sites. J Gen Virol. 1985 Dec;66(Pt 12):2659–2670. doi: 10.1099/0022-1317-66-12-2659. [DOI] [PubMed] [Google Scholar]
  29. Umene K. Recombination of the internal direct repeat element DR2 responsible for the fluidity of the a sequence of herpes simplex virus type 1. J Virol. 1991 Oct;65(10):5410–5416. doi: 10.1128/jvi.65.10.5410-5416.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Umene K. Short, duplicated sequence indicative of the recombinogenicity of the junction between a unique and an inverted repeat sequence in the S component of the herpes simplex virus type 1 genome. J Virol. 1989 May;63(5):1877–1883. doi: 10.1128/jvi.63.5.1877-1883.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Umene K. Transition from a heterozygous to a homozygous state of a pair of loci in the inverted repeat sequences of the L component of the herpes simplex virus type 1 genome. J Virol. 1987 Apr;61(4):1187–1192. doi: 10.1128/jvi.61.4.1187-1192.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Umene K. Variability of the region of the herpes simplex virus type 1 genome yielding defective DNA: SmaI fragment polymorphism. Intervirology. 1985;23(3):131–139. doi: 10.1159/000149596. [DOI] [PubMed] [Google Scholar]
  33. Umene K., Yoshida M. Genomic characterization of two predominant genotypes of herpes simplex virus type 1. Arch Virol. 1993;131(1-2):29–46. doi: 10.1007/BF01379078. [DOI] [PubMed] [Google Scholar]
  34. Umene K., Yoshida M. Reiterated sequences of herpes simplex virus type 1 (HSV-1) genome can serve as physical markers for the differentiation of HSV-1 strains. Arch Virol. 1989;106(3-4):281–299. doi: 10.1007/BF01313958. [DOI] [PubMed] [Google Scholar]
  35. Varmuza S. L., Smiley J. R. Signals for site-specific cleavage of HSV DNA: maturation involves two separate cleavage events at sites distal to the recognition sequences. Cell. 1985 Jul;41(3):793–802. doi: 10.1016/s0092-8674(85)80060-x. [DOI] [PubMed] [Google Scholar]
  36. Weber P. C., Challberg M. D., Nelson N. J., Levine M., Glorioso J. C. Inversion events in the HSV-1 genome are directly mediated by the viral DNA replication machinery and lack sequence specificity. Cell. 1988 Jul 29;54(3):369–381. doi: 10.1016/0092-8674(88)90200-0. [DOI] [PubMed] [Google Scholar]
  37. Weber P. C., Levine M., Glorioso J. C. Recombinogenic properties of herpes simplex virus type 1 DNA sequences resident in simian virus 40 minichromosomes. J Virol. 1990 Jan;64(1):300–306. doi: 10.1128/jvi.64.1.300-306.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Wells R. D., Collier D. A., Hanvey J. C., Shimizu M., Wohlrab F. The chemistry and biology of unusual DNA structures adopted by oligopurine.oligopyrimidine sequences. FASEB J. 1988 Nov;2(14):2939–2949. [PubMed] [Google Scholar]
  39. Wohlrab F., Chatterjee S., Wells R. D. The herpes simplex virus 1 segment inversion site is specifically cleaved by a virus-induced nuclear endonuclease. Proc Natl Acad Sci U S A. 1991 Aug 1;88(15):6432–6436. doi: 10.1073/pnas.88.15.6432. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Wohlrab F., McLean M. J., Wells R. D. The segment inversion site of herpes simplex virus type 1 adopts a novel DNA structure. J Biol Chem. 1987 May 5;262(13):6407–6416. [PubMed] [Google Scholar]

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