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. 1989 Sep;86(17):6518–6522. doi: 10.1073/pnas.86.17.6518

Cellular proteins specifically bind single- and double-stranded DNA and RNA from the initiation site of a transcript that crosses the origin of DNA replication of herpes simplex virus 1.

R J Roller 1, A L McCormick 1, B Roizman 1
PMCID: PMC297875  PMID: 2549540

Abstract

The small-component origins of herpes simplex virus 1 DNA synthesis are transcribed late in infection by an RNA with heterogeneous initiation sites approximately 290-360 base pairs from the origins. We report that cellular proteins react with a labeled RNA probe representing the 5' terminus of a subset of this RNA but not with the complementary strand of this RNA. The proteins form two complexes. Complex 2 was formed by all nuclear extracts tested, whereas complex 1 was invariably formed by proteins present only in nuclear extracts of mock-infected cells. Complex 1 protects a contiguous stretch of 40 nucleotides of the labeled RNA probe from nuclease degradation. Formation of complex 1 was competitively inhibited in a sequence-specific fashion by single-stranded RNA and DNA and by double-stranded RNA and DNA. The protein(s) forming complex 1 is, thus, quite distinct from known nucleic acid-binding proteins in that they recognize a specific nucleotide sequence, irrespective of the nature (single- and double-stranded RNA and DNA) of the nucleic acid. We conclude the following: (i) the proteins forming complex 1 and 2 are probably different, (ii) complex 1 is neither required throughout infection for viral replication nor able to hinder viral replication in cells in culture, and (iii) cells susceptible to infection encode one or more proteins that recognize specific sequences in single-stranded nucleic acids; either these proteins impart a compatible conformation on single-stranded nucleic acids with the conformation of the same strand in the double-stranded nucleic acid, or these proteins confer a specific, distinct conformation to both single-stranded and double-stranded nucleic acids.

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Selected References

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

  1. Aboul-ela F., Varani G., Walker G. T., Tinoco I., Jr The TFIIIA recognition fragment d(GGATGGGAG).d(CTCCCATCC) is B-form in solution. Nucleic Acids Res. 1988 Apr 25;16(8):3559–3572. doi: 10.1093/nar/16.8.3559. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Ackermann M., Chou J., Sarmiento M., Lerner R. A., Roizman B. Identification by antibody to a synthetic peptide of a protein specified by a diploid gene located in the terminal repeats of the L component of herpes simplex virus genome. J Virol. 1986 Jun;58(3):843–850. doi: 10.1128/jvi.58.3.843-850.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Arsenakis M., Hubenthal-Voss J., Campadelli-Fiume G., Pereira L., Roizman B. Construction and properties of a cell line constitutively expressing the herpes simplex virus glycoprotein B dependent on functional alpha 4 protein synthesis. J Virol. 1986 Nov;60(2):674–682. doi: 10.1128/jvi.60.2.674-682.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Arsenakis M., Roizman B. A post-alpha gene function turns off the capacity of a host protein to bind DNA in cells infected with herpes simplex virus 1. J Virol. 1984 Mar;49(3):813–818. doi: 10.1128/jvi.49.3.813-818.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Bandziulis R. J., Swanson M. S., Dreyfuss G. RNA-binding proteins as developmental regulators. Genes Dev. 1989 Apr;3(4):431–437. doi: 10.1101/gad.3.4.431. [DOI] [PubMed] [Google Scholar]
  6. Bugler B., Bourbon H., Lapeyre B., Wallace M. O., Chang J. H., Amalric F., Olson M. O. RNA binding fragments from nucleolin contain the ribonucleoprotein consensus sequence. J Biol Chem. 1987 Aug 15;262(23):10922–10925. [PubMed] [Google Scholar]
  7. 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]
  8. Ejercito P. M., Kieff E. D., Roizman B. Characterization of herpes simplex virus strains differing in their effects on social behaviour of infected cells. J Gen Virol. 1968 May;2(3):357–364. doi: 10.1099/0022-1317-2-3-357. [DOI] [PubMed] [Google Scholar]
  9. Fairall L., Rhodes D., Klug A. Mapping of the sites of protection on a 5 S RNA gene by the Xenopus transcription factor IIIA. A model for the interaction. J Mol Biol. 1986 Dec 5;192(3):577–591. doi: 10.1016/0022-2836(86)90278-0. [DOI] [PubMed] [Google Scholar]
  10. Fenwick M., Morse L. S., Roizman B. Anatomy of herpes simplex virus DNA. XI. Apparent clustering of functions effecting rapid inhibition of host DNA and protein synthesis. J Virol. 1979 Feb;29(2):825–827. doi: 10.1128/jvi.29.2.825-827.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Hanas J. S., Bogenhagen D. F., Wu C. W. Binding of Xenopus transcription factor A to 5S RNA and to single stranded DNA. Nucleic Acids Res. 1984 Mar 26;12(6):2745–2758. doi: 10.1093/nar/12.6.2745. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Honess R. W., Roizman B. Regulation of herpesvirus macromolecular synthesis. I. Cascade regulation of the synthesis of three groups of viral proteins. J Virol. 1974 Jul;14(1):8–19. doi: 10.1128/jvi.14.1.8-19.1974. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Honess R. W., Roizman B. Regulation of herpesvirus macromolecular synthesis: sequential transition of polypeptide synthesis requires functional viral polypeptides. Proc Natl Acad Sci U S A. 1975 Apr;72(4):1276–1280. doi: 10.1073/pnas.72.4.1276. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Hubenthal-Voss J., Starr L., Roizman B. The herpes simplex virus origins of DNA synthesis in the S component are each contained in a transcribed open reading frame. J Virol. 1987 Nov;61(11):3349–3355. doi: 10.1128/jvi.61.11.3349-3355.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Knipe D. M., Ruyechan W. T., Roizman B., Halliburton I. W. Molecular genetics of herpes simplex virus: demonstration of regions of obligatory and nonobligatory identity within diploid regions of the genome by sequence replacement and insertion. Proc Natl Acad Sci U S A. 1978 Aug;75(8):3896–3900. doi: 10.1073/pnas.75.8.3896. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Konarska M. M., Sharp P. A. Electrophoretic separation of complexes involved in the splicing of precursors to mRNAs. Cell. 1986 Sep 12;46(6):845–855. doi: 10.1016/0092-8674(86)90066-8. [DOI] [PubMed] [Google Scholar]
  17. Kristie T. M., Roizman B. Alpha 4, the major regulatory protein of herpes simplex virus type 1, is stably and specifically associated with promoter-regulatory domains of alpha genes and of selected other viral genes. Proc Natl Acad Sci U S A. 1986 May;83(10):3218–3222. doi: 10.1073/pnas.83.10.3218. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Lee K. A., Bindereif A., Green M. R. A small-scale procedure for preparation of nuclear extracts that support efficient transcription and pre-mRNA splicing. Gene Anal Tech. 1988 Mar-Apr;5(2):22–31. doi: 10.1016/0735-0651(88)90023-4. [DOI] [PubMed] [Google Scholar]
  19. Mavromara-Nazos P., Ackermann M., Roizman B. Construction and properties of a viable herpes simplex virus 1 recombinant lacking coding sequences of the alpha 47 gene. J Virol. 1986 Nov;60(2):807–812. doi: 10.1128/jvi.60.2.807-812.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Mavromara-Nazos P., Silver S., Hubenthal-Voss J., McKnight J. L., Roizman B. Regulation of herpes simplex virus 1 genes: alpha gene sequence requirements for transient induction of indicator genes regulated by beta or late (gamma 2) promoters. Virology. 1986 Mar;149(2):152–164. doi: 10.1016/0042-6822(86)90117-0. [DOI] [PubMed] [Google Scholar]
  21. McCall M., Brown T., Hunter W. N., Kennard O. The crystal structure of d(GGATGGGAG): an essential part of the binding site for transcription factor IIIA. Nature. 1986 Aug 14;322(6080):661–664. doi: 10.1038/322661a0. [DOI] [PubMed] [Google Scholar]
  22. McGeoch D. J., Dalrymple M. A., Davison A. J., Dolan A., Frame M. C., McNab D., Perry L. J., Scott J. E., Taylor P. The complete DNA sequence of the long unique region in the genome of herpes simplex virus type 1. J Gen Virol. 1988 Jul;69(Pt 7):1531–1574. doi: 10.1099/0022-1317-69-7-1531. [DOI] [PubMed] [Google Scholar]
  23. Mocarski E. S., Roizman B. Herpesvirus-dependent amplification and inversion of cell-associated viral thymidine kinase gene flanked by viral a sequences and linked to an origin of viral DNA replication. Proc Natl Acad Sci U S A. 1982 Sep;79(18):5626–5630. doi: 10.1073/pnas.79.18.5626. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Nielsen D. A., Shapiro D. J. Preparation of capped RNA transcripts using T7 RNA polymerase. Nucleic Acids Res. 1986 Jul 25;14(14):5936–5936. doi: 10.1093/nar/14.14.5936. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Olson M. O., Rivers Z. M., Thompson B. A., Kao W. Y., Case S. T. Interaction of nucleolar phosphoprotein C23 with cloned segments of rat ribosomal deoxyribonucleic acid. Biochemistry. 1983 Jul 5;22(14):3345–3351. doi: 10.1021/bi00283a007. [DOI] [PubMed] [Google Scholar]
  26. Pelham H. R., Brown D. D. A specific transcription factor that can bind either the 5S RNA gene or 5S RNA. Proc Natl Acad Sci U S A. 1980 Jul;77(7):4170–4174. doi: 10.1073/pnas.77.7.4170. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Piñol-Roma S., Choi Y. D., Matunis M. J., Dreyfuss G. Immunopurification of heterogeneous nuclear ribonucleoprotein particles reveals an assortment of RNA-binding proteins. Genes Dev. 1988 Feb;2(2):215–227. doi: 10.1101/gad.2.2.215. [DOI] [PubMed] [Google Scholar]
  28. Post L. E., Roizman B. A generalized technique for deletion of specific genes in large genomes: alpha gene 22 of herpes simplex virus 1 is not essential for growth. Cell. 1981 Jul;25(1):227–232. doi: 10.1016/0092-8674(81)90247-6. [DOI] [PubMed] [Google Scholar]
  29. Rhodes D., Klug A. An underlying repeat in some transcriptional control sequences corresponding to half a double helical turn of DNA. Cell. 1986 Jul 4;46(1):123–132. doi: 10.1016/0092-8674(86)90866-4. [DOI] [PubMed] [Google Scholar]
  30. Richardson J. P. Activation of rho protein ATPase requires simultaneous interaction at two kinds of nucleic acid-binding sites. J Biol Chem. 1982 May 25;257(10):5760–5766. [PubMed] [Google Scholar]
  31. Roizman B., Spear P. G. Preparation of herpes simplex virus of high titer. J Virol. 1968 Jan;2(1):83–84. doi: 10.1128/jvi.2.1.83-84.1968. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. 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]
  33. Stow N. D. Localization of an origin of DNA replication within the TRS/IRS repeated region of the herpes simplex virus type 1 genome. EMBO J. 1982;1(7):863–867. doi: 10.1002/j.1460-2075.1982.tb01261.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Swanson M. S., Nakagawa T. Y., LeVan K., Dreyfuss G. Primary structure of human nuclear ribonucleoprotein particle C proteins: conservation of sequence and domain structures in heterogeneous nuclear RNA, mRNA, and pre-rRNA-binding proteins. Mol Cell Biol. 1987 May;7(5):1731–1739. doi: 10.1128/mcb.7.5.1731. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Voss J. H., Roizman B. Properties of two 5'-coterminal RNAs transcribed part way and across the S component origin of DNA synthesis of the herpes simplex virus 1 genome. Proc Natl Acad Sci U S A. 1988 Nov;85(22):8454–8458. doi: 10.1073/pnas.85.22.8454. [DOI] [PMC free article] [PubMed] [Google Scholar]

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