Skip to main content
NCBI home page
Journal of Virology logoLink to Journal of Virology
. 1989 Feb;63(2):523–531. doi: 10.1128/jvi.63.2.523-531.1989

Genome structure of cottontail rabbit herpesvirus.

J Cebrian 1, N Berthelot 1, M Laithier 1
PMCID: PMC247720  PMID: 2911115

Abstract

The genome structure of a herpesvirus isolated from primary cultures of kidney cells from the cottontail rabbit Sylvilagus floridanus was elucidated by using electron microscopy and restriction enzyme analysis. The genome, which was about 150 kilobase pairs long and which had an average G + C composition of 45%, consisted of two regions with unique base sequences (54 and 47 kilobase pairs) enclosed by reiterations of a 925-base-pair sequence with a variable copy number. The internal repeats were in opposite polarity with respect to the terminal repeats, and both unique regions underwent inversion. The nucleotide sequence of the repeat unit was determined, and virion DNA termini were precisely localized within this sequence. Elements showing homology with the cleavage-packaging signals common to other herpesviruses were detected. The data indicate that this virus is different from the previously described herpesvirus sylvilagus.

Full text

PDF
523

Images in this article

526Image
on p.526
527Image
on p.527
528Image
on p.528
530Image
on p.530

Selected References

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

  1. BRENNER S., HORNE R. W. A negative staining method for high resolution electron microscopy of viruses. Biochim Biophys Acta. 1959 Jul;34:103–110. doi: 10.1016/0006-3002(59)90237-9. [DOI] [PubMed] [Google Scholar]
  2. Bankier A. T., Dietrich W., Baer R., Barrell B. G., Colbère-Garapin F., Fleckenstein B., Bodemer W. Terminal repetitive sequences in herpesvirus saimiri virion DNA. J Virol. 1985 Jul;55(1):133–139. doi: 10.1128/jvi.55.1.133-139.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Ben-Porat T., Kaplan A. S., Stehn B., Rubenstein A. S. Concatemeric forms of intracellular herpesvirus DNA. Virology. 1976 Feb;69(2):547–560. doi: 10.1016/0042-6822(76)90484-0. [DOI] [PubMed] [Google Scholar]
  4. Ben-Porat T., Rixon F. J. Replication of herpesvirus DNA. IV: analysis of concatemers. Virology. 1979 Apr 15;94(1):61–70. doi: 10.1016/0042-6822(79)90438-0. [DOI] [PubMed] [Google Scholar]
  5. Biggin M. D., Gibson T. J., Hong G. F. Buffer gradient gels and 35S label as an aid to rapid DNA sequence determination. Proc Natl Acad Sci U S A. 1983 Jul;80(13):3963–3965. doi: 10.1073/pnas.80.13.3963. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Bornkamm G. W., Delius H., Fleckenstein B., Werner F. J., Mulder C. Structure of Herpesvirus saimiri genomes: arrangement of heavy and light sequences in the M genome. J Virol. 1976 Jul;19(1):154–161. doi: 10.1128/jvi.19.1.154-161.1976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Cebrian J., Bucchini D., Sheldrick P. "Endless" viral DNA in cells infected with channel catfish virus. J Virol. 1983 May;46(2):405–412. doi: 10.1128/jvi.46.2.405-412.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Church G. M., Gilbert W. Genomic sequencing. Proc Natl Acad Sci U S A. 1984 Apr;81(7):1991–1995. doi: 10.1073/pnas.81.7.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Cohrs R., Rouhandeh H. Characterization of the genome of Herpesvirus sylvilagus. Intervirology. 1987;28(3):181–184. doi: 10.1159/000150014. [DOI] [PubMed] [Google Scholar]
  10. Cohrs R., Rouhandeh H. Herpesvirus sylvilagus I. Polypeptides of virions and nucleocapsids. J Virol. 1982 Mar;41(3):1063–1072. doi: 10.1128/jvi.41.3.1063-1072.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Davison A. J. Structure of the genome termini of varicella-zoster virus. J Gen Virol. 1984 Nov;65(Pt 11):1969–1977. doi: 10.1099/0022-1317-65-11-1969. [DOI] [PubMed] [Google Scholar]
  12. 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]
  13. Delius H., Clements J. B. A partial denaturation map of herpes simplex virus type 1 DNA: evidence for inversions of the unique DNA regions. J Gen Virol. 1976 Oct;33(1):125–133. doi: 10.1099/0022-1317-33-1-125. [DOI] [PubMed] [Google Scholar]
  14. Fleckenstein B., Bornkamm G. W., Ludwig H. Repetitive sequences in complete and defective genomes of Herpesvirus saimiri. J Virol. 1975 Feb;15(2):398–406. doi: 10.1128/jvi.15.2.398-406.1975. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Fleckenstein B. Oncogenic herpesviruses of non-human primates. Biochim Biophys Acta. 1979 Nov 30;560(3):301–342. doi: 10.1016/0304-419x(79)90007-6. [DOI] [PubMed] [Google Scholar]
  16. Given D., Yee D., Griem K., Kieff E. DNA of Epstein-Barr virus. V. Direct repeats of the ends of Epstein-Barr virus DNA. J Virol. 1979 Jun;30(3):852–862. doi: 10.1128/jvi.30.3.852-862.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Hammerschmidt W., Ludwig H., Buhk H. J. Specificity of cleavage in replicative-form DNA of bovine herpesvirus 1. J Virol. 1988 Apr;62(4):1355–1363. doi: 10.1128/jvi.62.4.1355-1363.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Hayward G. S., Jacob R. J., Wadsworth S. C., Roizman B. Anatomy of herpes simplex virus DNA: evidence for four populations of molecules that differ in the relative orientations of their long and short components. Proc Natl Acad Sci U S A. 1975 Nov;72(11):4243–4247. doi: 10.1073/pnas.72.11.4243. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Hinze H. C. Induction of lymphoid hyperplasia and lymphoma-like disease in rabbits by Herpesvirus sylvilagus. Int J Cancer. 1971 Nov 15;8(3):514–522. doi: 10.1002/ijc.2910080320. [DOI] [PubMed] [Google Scholar]
  20. Hinze H. C. New member of the herpesvirus group isolated from wild cottontail rabbits. Infect Immun. 1971 Feb;3(2):350–354. doi: 10.1128/iai.3.2.350-354.1971. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Honess R. W. Herpes simplex and 'the herpes complex': diverse observations and a unifying hypothesis. The eighth Fleming lecture. J Gen Virol. 1984 Dec;65(Pt 12):2077–2107. doi: 10.1099/0022-1317-65-12-2077. [DOI] [PubMed] [Google Scholar]
  22. Inman R. B. A denaturation map of the lambda phage DNA molecule determined by electron microscopy. J Mol Biol. 1966 Jul;18(3):464–476. doi: 10.1016/s0022-2836(66)80037-2. [DOI] [PubMed] [Google Scholar]
  23. Jacob R. J., Morse L. S., Roizman B. Anatomy of herpes simplex virus DNA. XII. Accumulation of head-to-tail concatemers in nuclei of infected cells and their role in the generation of the four isomeric arrangements of viral DNA. J Virol. 1979 Feb;29(2):448–457. doi: 10.1128/jvi.29.2.448-457.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Kintner C. R., Sugden B. The structure of the termini of the DNA of Epstein-Barr virus. Cell. 1979 Jul;17(3):661–671. doi: 10.1016/0092-8674(79)90273-3. [DOI] [PubMed] [Google Scholar]
  25. Kramp W. J., Medveczky P., Mulder C., Hinze H. C., Sullivan J. L. Herpesvirus sylvilagus infects both B and T lymphocytes in vivo. J Virol. 1985 Oct;56(1):60–65. doi: 10.1128/jvi.56.1.60-65.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. LaFemina R. L., Hayward G. S. Replicative forms of human cytomegalovirus DNA with joined termini are found in permissively infected human cells but not in non-permissive Balb/c-3T3 mouse cells. J Gen Virol. 1983 Feb;64(Pt 2):373–389. doi: 10.1099/0022-1317-64-2-373. [DOI] [PubMed] [Google Scholar]
  27. Ladin B. F., Blankenship M. L., Ben-Porat T. Replication of herpesvirus DNA. V. Maturation of concatemeric DNA of pseudorabies virus to genome length is related to capsid formation. J Virol. 1980 Mar;33(3):1151–1164. doi: 10.1128/jvi.33.3.1151-1164.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Marks J. R., Spector D. H. Replication of the murine cytomegalovirus genome: structure and role of the termini in the generation and cleavage of concatenates. Virology. 1988 Jan;162(1):98–107. doi: 10.1016/0042-6822(88)90398-4. [DOI] [PubMed] [Google Scholar]
  29. Medveczky P., Kramp W. J., Sullivan J. L. Circular Herpesvirus sylvilagus DNA in spleen cells of experimentally infected cottontail rabbits. J Virol. 1984 Nov;52(2):711–714. doi: 10.1128/jvi.52.2.711-714.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. 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]
  31. Pettersson U., Mulder C., Deluis H., Sharp P. A. Cleavage of adenovirus type 2 DNA into six unique fragments by endonuclease R-RI. Proc Natl Acad Sci U S A. 1973 Jan;70(1):200–204. doi: 10.1073/pnas.70.1.200. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Rouhandeh H., Cohrs R. Cloning and physical mapping of Herpesvirus sylvilagus DNA. Gene. 1987;61(1):31–39. doi: 10.1016/0378-1119(87)90362-3. [DOI] [PubMed] [Google Scholar]
  33. Sanger F., Coulson A. R., Friedmann T., Air G. M., Barrell B. G., Brown N. L., Fiddes J. C., Hutchison C. A., 3rd, Slocombe P. M., Smith M. The nucleotide sequence of bacteriophage phiX174. J Mol Biol. 1978 Oct 25;125(2):225–246. doi: 10.1016/0022-2836(78)90346-7. [DOI] [PubMed] [Google Scholar]
  34. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Sheldrick P., Laithier M., Lando D., Ryhiner M. L. Infectious DNA from herpes simplex virus: infectivity of double-stranded and single-stranded molecules. Proc Natl Acad Sci U S A. 1973 Dec;70(12):3621–3625. doi: 10.1073/pnas.70.12.3621. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Stow N. D., McMonagle E. C., Davison A. J. Fragments from both termini of the herpes simplex virus type 1 genome contain signals required for the encapsidation of viral DNA. Nucleic Acids Res. 1983 Dec 10;11(23):8205–8220. doi: 10.1093/nar/11.23.8205. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Tamashiro J. C., Spector D. H. Terminal structure and heterogeneity in human cytomegalovirus strain AD169. J Virol. 1986 Sep;59(3):591–604. doi: 10.1128/jvi.59.3.591-604.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. 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]
  39. 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]
  40. Vlazny D. A., Frenkel N. Replication of herpes simplex virus DNA: localization of replication recognition signals within defective virus genomes. Proc Natl Acad Sci U S A. 1981 Feb;78(2):742–746. doi: 10.1073/pnas.78.2.742. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Vlazny D. A., Kwong A., Frenkel N. Site-specific cleavage/packaging of herpes simplex virus DNA and the selective maturation of nucleocapsids containing full-length viral DNA. Proc Natl Acad Sci U S A. 1982 Mar;79(5):1423–1427. doi: 10.1073/pnas.79.5.1423. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Wilkie N. M. Physical maps for Herpes simplex virus type 1 DNA for restriction endonucleases Hind III, Hpa-1, and X. bad. J Virol. 1976 Oct;20(1):222–233. doi: 10.1128/jvi.20.1.222-233.1976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Yanisch-Perron C., Vieira J., Messing J. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene. 1985;33(1):103–119. doi: 10.1016/0378-1119(85)90120-9. [DOI] [PubMed] [Google Scholar]

Articles from Journal of Virology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES