Home LiteratureArticle Details
PMID: 9765421 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.

In vitro processing of herpes simplex virus type 1 DNA replication intermediates by the viral alkaline nuclease, UL12.

Journal of virology ·Vol. 72 ·No. 11 ·1998-11-00 ·Pages 8772-81

Goldstein JN, Weller SK

Abstract

Herpes simplex virus type 1 (HSV-1) DNA replication intermediates exist in a complex nonlinear structure that does not migrate into a pulsed-field gel. Genetic evidence suggests that the product of the UL12 gene, termed alkaline nuclease, plays a role in processing replication intermediates (R. Martinez, R. T. Sarisky, P. C. Weber, and S. K. Weller, J. Virol. 70:2075-2085, 1996). In this study we have tested the hypothesis that alkaline nuclease acts as a structure-specific resolvase. Cruciform structures generated with oligonucleotides were treated with purified alkaline nuclease; however, instead of being resolved into linear duplexes as would be expected of a resolvase activity, the artificial cruciforms were degraded. DNA replication intermediates were isolated from the well of a pulsed-field gel ("well DNA") and treated with purified HSV-1 alkaline nuclease. Although alkaline nuclease can degrade virion DNA to completion, digestion of well DNA results in a smaller-than-unit-length product that migrates as a heterogeneous smear; this product is resistant to further digestion by alkaline nuclease. The smaller-than-unit-length products are representative of the entire HSV genome, indicating that alkaline nuclease is not inhibited at specific sequences. To further probe the structure of replicating DNA, well DNA was treated with various known nucleases; our results indicate that replicating DNA apparently contains no accessible double-stranded ends but does contain nicks and gaps. Our data suggest that UL12 functions at nicks and gaps in replicating DNA to correctly repair or process the replicating genome into a form suitable for encapsidation.

MeSH Terms
Animals Base Sequence Chlorocebus aethiops DNA Replication DNA, Single-Stranded/chemistry,genetics,metabolism DNA, Viral/chemistry,genetics,metabolism Electrophoresis, Gel, Pulsed-Field Herpesvirus 1, Human/genetics,metabolism In Vitro Techniques Oligodeoxyribonucleotides/genetics Recombinases Ribonucleases/metabolism Transposases/metabolism Vero Cells
Chemicals
DNA, Single-Stranded DNA, Viral Oligodeoxyribonucleotides Recombinases Transposases Ribonucleases viral alkaline nuclease
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Goldstein J N
Department of Microbiology, University of Connecticut Health Center, Farmington, Connecticut 06030, USA.
Weller S K
References (79)
79 references, click to expand
  1. Identification of novel herpes simplex virus replicative intermediates by field inversion gel electrophoresis: implications for viral DNA amplification strategies.
    Virology. 1994 Aug 1;202(2):530-9 PMID: 8030219
  2. Herpes simplex virus replicative concatemers contain L components in inverted orientation.
    Virology. 1994 Sep;203(2):384-8 PMID: 8053162
  3. Rolling circle DNA replication in vitro by a complex of herpes simplex virus type 1-encoded enzymes.
    Proc Natl Acad Sci U S A. 1994 Oct 25;91(22):10665-9 PMID: 7938010
  4. Biochemistry of homologous recombination in Escherichia coli.
    Microbiol Rev. 1994 Sep;58(3):401-65 PMID: 7968921
  5. Endo-exonucleases: enzymes involved in DNA repair and cell death?
    Bioessays. 1994 Oct;16(10):761-6 PMID: 7980480
  6. Separation of large DNA molecules with high voltage pulsed field gel electrophoresis.
    Electrophoresis. 1994 Aug-Sep;15(8-9):1078-83 PMID: 7859711
  7. Enhancement of RecA strand-transfer activity by the RecJ exonuclease of Escherichia coli.
    J Biol Chem. 1995 Mar 24;270(12):6881-5 PMID: 7896836
  8. Herpes simplex virus type 1 DNA replication is specifically required for high-frequency homologous recombination between repeated sequences.
    J Virol. 1995 May;69(5):3084-9 PMID: 7707536
  9. Molecular phylogeny and evolutionary timescale for the family of mammalian herpesviruses.
    J Mol Biol. 1995 Mar 31;247(3):443-58 PMID: 7714900
  10. Characterization of Epstein-Barr virus DNase and its interaction with the major DNA binding protein.
    Virology. 1995 Apr 20;208(2):712-22 PMID: 7747443
  11. Rolling circle DNA replication by extracts of herpes simplex virus type 1-infected human cells.
    J Virol. 1996 Feb;70(2):1132-6 PMID: 8551573
  12. The product of a 1.9-kb mRNA which overlaps the HSV-1 alkaline nuclease gene (UL12) cannot relieve the growth defects of a null mutant.
    Virology. 1996 Jan 15;215(2):152-64 PMID: 8560762
  13. Herpes simplex virus type 1 alkaline nuclease is required for efficient processing of viral DNA replication intermediates.
    J Virol. 1996 Apr;70(4):2075-85 PMID: 8642627
  14. Branched structures in the intracellular DNA of herpes simplex virus type 1.
    J Virol. 1996 May;70(5):3169-75 PMID: 8627797
  15. Purification and characterization of herpes simplex virus type 1 alkaline exonuclease expressed in Escherichia coli.
    J Virol. 1996 Mar;70(3):2008-13 PMID: 8627727
  16. The structure and isomerization of herpes simplex virus genomes.
    Cell. 1979 Mar;16(3):481-94 PMID: 222462
  17. Electron microscopic mapping of proteins bound to herpes simplex virus DNA.
    Nucleic Acids Res. 1979 Aug 10;6(11):3427-41 PMID: 226938
  18. BamI, KpnI, and SalI restriction enzyme maps of the DNAs of herpes simplex virus strains Justin and F: occurrence of heterogeneities in defined regions of the viral DNA.
    J Virol. 1979 Nov;32(2):429-41 PMID: 228068
  19. DNase induced after infection of KB cells by herpes simplex virus type 1 or type 2. II. Characterization of an associated endonuclease activity.
    J Virol. 1979 Nov;32(2):449-57 PMID: 228069
  20. Alkaline deoxyribonuclease induced by herpes simplex virus type 1: composition and properties of the purified enzyme.
    Virology. 1980 Jun;103(2):493-501 PMID: 6247825
  21. Identification of proteins tightly bound to herpes simplex virus DNA.
    Virology. 1980 Aug;105(1):254-5 PMID: 6251609
  22. Cloning of reiterated and nonreiterated herpes simplex virus 1 sequences as BamHI fragments.
    Proc Natl Acad Sci U S A. 1980 Jul;77(7):4201-5 PMID: 6254015
  23. Mechanism of degradation of duplex DNA by the DNase induced by herpes simplex virus.
    J Virol. 1981 Jun;38(3):1005-14 PMID: 6264148
  24. 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):1423-7 PMID: 6280181
  25. T4 endonuclease VII cleaves holliday structures.
    Cell. 1982 Jun;29(2):357-65 PMID: 6288255
  26. Genetic analysis of temperature-sensitive mutants which define the gene for the major herpes simplex virus type 1 DNA-binding protein.
    J Virol. 1983 Jan;45(1):354-66 PMID: 6296442
  27. A noninverting genome of a viable herpes simplex virus 1: presence of head-to-tail linkages in packaged genomes and requirements for circularization after infection.
    J Virol. 1985 Feb;53(2):587-95 PMID: 2982037
  28. 3' homologous free ends are required for stable joint molecule formation by the RecA and single-stranded binding proteins of Escherichia coli.
    Proc Natl Acad Sci U S A. 1987 Feb;84(3):690-4 PMID: 3543934
  29. Visualization of replicating mammalian and T4 bacteriophage DNA.
    Cold Spring Harb Symp Quant Biol. 1968;33:509-24 PMID: 4239597
  30. Size, composition, and structure of the deoxyribonucleic acid of herpes simplex virus subtypes 1 and 2.
    J Virol. 1971 Aug;8(2):125-32 PMID: 4329966
  31. A deoxyribonuclease which requires nucleoside triphosphate from Micrococcus lysodeikticus. IV. The mode of DNA hydrolysis.
    Biochim Biophys Acta. 1972 May 29;269(3):347-53 PMID: 5039540
  32. Separation of the herpesvirus deoxyribonucleic acid duplex into unique fragments and intact strand on sedimentation in alkaline gradients.
    J Virol. 1972 Oct;10(4):565-72 PMID: 4343538
  33. Isolation of circular DNA molecules from whole cellular DNA by use of ATP-dependent deoxyribonuclease.
    Proc Natl Acad Sci U S A. 1973 Oct;70(10):2884-7 PMID: 4355370
  34. The synthesis and substructure of herpesvirus DNA: the distribution of alkali-labile single strand interruptions in HSV-1 DNA.
    J Gen Virol. 1973 Dec;21(3):453-67 PMID: 4357936
  35. Human cytomegalovirus. II. Lack of relatedness to DNA of herpes simples I and II, Epstein-Barr virus, and nonhuman strains of cytomegalovirus.
    J Virol. 1974 Mar;13(3):642-5 PMID: 4362866
  36. The structure and biological properties of herpes simplex virus DNA.
    Cold Spring Harb Symp Quant Biol. 1975;39 Pt 2:657-66 PMID: 169021
  37. Replication intermediates of herpes simplex virus DNA.
    Virology. 1976 Feb;69(2):647-59 PMID: 176788
  38. Function of gene 49 of bacteriophage T4. II. Analysis of intracellular development and the structure of very fast-sedimenting DNA.
    J Virol. 1976 Jun;18(3):1000-15 PMID: 775128
  39. Fate of parental herpesvirus DNA.
    Virology. 1976 Jun;71(2):412-22 PMID: 180660
  40. Replicating DNA of herpes simplex virus type 1.
    Intervirology. 1976;7(3):155-75 PMID: 187556
  41. In vitro repair of the preexisting nicks and gaps in herpes simplex virus DNA.
    Virology. 1977 Jan;76(1):286-94 PMID: 189493
  42. Replication of herpesvirus DNA. I. Electron microscopic analysis of replicative structures.
    Virology. 1977 Jun 15;79(2):281-91 PMID: 194406
  43. Anatomy of herpes simplex virus DNA VIII. Properties of the replicating DNA.
    J Virol. 1977 Aug;23(2):394-411 PMID: 196115
  44. The deoxyribonuclease induced after infection of KB cells by herpes simplex virus type 1 or type 2. I. Purification and characterization of the enzyme.
    J Biol Chem. 1978 May 25;253(10):3557-62 PMID: 206546
  45. 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):448-57 PMID: 219240
  46. Isolation and characterization of herpes simplex virus type 1 host range mutants defective in viral DNA synthesis.
    J Virol. 1988 Jan;62(1):91-9 PMID: 2824860
  47. Characterization of intranuclear capsids made by ts morphogenic mutants of HSV-1.
    Virology. 1988 Apr;163(2):471-80 PMID: 2833020
  48. 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):369-81 PMID: 2840204
  49. Plasmid-like replicative intermediates of the Epstein-Barr virus lytic origin of DNA replication.
    J Virol. 1996 Jun;70(6):3423-31 PMID: 8648674
  50. Suppression of amber nonsense mutations of herpes simplex virus type 1 in a tissue culture system.
    J Gen Virol. 1996 Feb;77 ( Pt 2 ):199-209 PMID: 8627223
  51. Inhibition of topoisomerase II by ICRF-193 prevents efficient replication of herpes simplex virus type 1.
    J Virol. 1996 Jul;70(7):4523-9 PMID: 8676478
  52. Replication of herpes simplex virus type 1 DNA is inhibited in a temperature-sensitive mutant of BHK-21 cells lacking RCC1 (regulator of chromosome condensation) and virus DNA remains linear.
    J Gen Virol. 1996 Sep;77 ( Pt 9):2261-70 PMID: 8811026
  53. Herpes simplex virus type 1 replication and recombination.
    Biochimie. 1995;77(10):787-95 PMID: 8824776
  54. Evidence that the UL84 gene product of human cytomegalovirus is essential for promoting oriLyt-dependent DNA replication and formation of replication compartments in cotransfection assays.
    J Virol. 1996 Nov;70(11):7398-413 PMID: 8892858
  55. The herpes simplex virus type 1 UL6 protein is essential for cleavage and packaging but not for genomic inversion.
    Virology. 1996 Dec 15;226(2):403-7 PMID: 8955060
  56. The FEN-1 family of structure-specific nucleases in eukaryotic DNA replication, recombination and repair.
    Bioessays. 1997 Mar;19(3):233-40 PMID: 9080773
  57. The replicating intermediates of herpes simplex virus type 1 DNA are relatively short.
    J Neurovirol. 1995 Jun;1(2):165-76 PMID: 9222355
  58. Herpes simplex virus DNA replication.
    Annu Rev Biochem. 1997;66:347-84 PMID: 9242911
  59. The human cytomegalovirus UL98 gene encodes the conserved herpesvirus alkaline nuclease.
    J Gen Virol. 1997 Nov;78 ( Pt 11):2953-61 PMID: 9367383
  60. Structure-function analysis of the herpes simplex virus type 1 UL12 gene: correlation of deoxyribonuclease activity in vitro with replication function.
    Virology. 1998 Mar 30;243(1):247-59 PMID: 9527934
  61. The exonuclease activity of HSV-1 UL12 is required for in vivo function.
    Virology. 1998 May 10;244(2):442-57 PMID: 9601512
  62. Heteroduplex joint formation in Escherichia coli recombination is initiated by pairing of a 3'-ending strand.
    Proc Natl Acad Sci U S A. 1998 Jun 9;95(12):6909-14 PMID: 9618512
  63. Functional conservations of the alkaline nuclease of herpes simplex type 1 and human cytomegalovirus.
    Virology. 1998 Sep 30;249(2):460-70 PMID: 9791036
  64. Cytochemical study of the localization and organization of parental herpes simplex virus type I DNA during initial infection of the cell.
    Eur J Cell Biol. 1989 Oct;50(1):187-200 PMID: 2558887
  65. Comparison of exonucleolytic activities of herpes simplex virus type-1 DNA polymerase and DNase.
    Eur J Biochem. 1990 Jul 31;191(2):263-73 PMID: 2166660
  66. Large-scale preparation of T4 endonuclease VII from over-expressing bacteria.
    Eur J Biochem. 1990 Dec 27;194(3):779-84 PMID: 2269300
  67. The herpes simplex virus type 1 alkaline nuclease is not essential for viral DNA synthesis: isolation and characterization of a lacZ insertion mutant.
    J Gen Virol. 1990 Dec;71 ( Pt 12):2941-52 PMID: 2177086
  68. Identification and characterization of a novel non-infectious herpes simplex virus-related particle.
    J Gen Virol. 1991 Mar;72 ( Pt 3):661-8 PMID: 1848601
  69. The effects on strand exchange of 5' versus 3' ends of single-stranded DNA in RecA nucleoprotein filaments.
    J Mol Biol. 1991 Jun 20;219(4):645-54 PMID: 2056532
  70. Herpes simplex virus type 1 recombination: role of DNA replication and viral a sequences.
    J Virol. 1992 Jan;66(1):277-85 PMID: 1309247
  71. Association between the herpes simplex virus major DNA-binding protein and alkaline nuclease.
    J Virol. 1992 Feb;66(2):1152-61 PMID: 1309895
  72. Herpes simplex virus 1 alkaline nuclease is required for efficient egress of capsids from the nucleus.
    Virology. 1993 Sep;196(1):146-62 PMID: 8395111
  73. Function of gene 49 of bacteriophage T4 III. Isolation of Holliday structures from very fast-sedimenting DNA.
    Virology. 1993 Oct;196(2):910-3 PMID: 8372457
  74. Demonstration of circularization of herpes simplex virus DNA following infection using pulsed field gel electrophoresis.
    Virology. 1993 Nov;197(1):459-62 PMID: 8212585
  75. Eleven loci encoding trans-acting factors are required for transient complementation of human cytomegalovirus oriLyt-dependent DNA replication.
    J Virol. 1993 Dec;67(12):6979-88 PMID: 8230421
  76. Human cytomegalovirus DNA replicates after early circularization by concatemer formation, and inversion occurs within the concatemer.
    J Virol. 1994 Feb;68(2):1040-51 PMID: 8289333
  77. Substrate specificity of the Escherichia coli RuvC protein. Resolution of three- and four-stranded recombination intermediates.
    J Biol Chem. 1994 Feb 18;269(7):5195-201 PMID: 8106501
  78. Study of the structure of replicative intermediates of HSV-1 DNA by pulsed-field gel electrophoresis.
    Virology. 1994 May 1;200(2):428-35 PMID: 8178432
  79. Mutagenesis and characterization of a 41-kilobase-pair region of the pseudorabies virus genome: transcription map, search for virulence genes, and comparison with homologs of herpes simplex virus type 1.
    Virology. 1994 May 1;200(2):784-90 PMID: 8178460
Article Info
Journal
Journal of virology
Abbr.
J Virol
ISSN
0022-538X
DOI
10.1128/JVI.72.11.8772-8781.1998
Published
1998-11-00
Pages
8772-81
Language
English
Region
United States
NLM ID
0113724
PMCID
PMC110293
Subset
IM
Grants
NIAID NIH HHS · R37 AI021747 · United States
NIAID NIH HHS · R01 AI021747 · United States
NIAID NIH HHS · R01 AI037549 · United States
NIAID NIH HHS · AI37549 · United States
NIAID NIH HHS · R56 AI037549 · United States
NIAID NIH HHS · AI21747 · United States
External Links
PubMed source DOI: 10.1128/JVI.72.11.8772-8781.1998 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2