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. 1984 Feb 24;12(4):2061–2079. doi: 10.1093/nar/12.4.2061

Replication origins and a sequence involved in coordinate induction of the immediate-early gene family are conserved in an intergenic region of herpes simplex virus.

J L Whitton, J B Clements
PMCID: PMC318641  PMID: 6322134

Abstract

We have determined the structure of the 5' portion of herpes simplex virus type 2 (HSF-2) immediate-early (IE) mRNA-3 and have obtained the DNA sequence specifying the N terminus of its encoded polypeptide, Vmw182, its untranslated leader and the intergenic region between IEmRNAs-3 & 4/5. Comparison of the HSV-2 intergenic sequences with the HSV-1 equivalent region identifies several conserved regions: (1) an AT-rich element with core consensus TAATGARAT which is likely to be the 'activator' sequence through which coordinate induction of the IE gene family is mediated. (2) GC-rich and GA-rich tracts, found in a wide variety of eukaryotic promoters, which vary in position and orientation between HSV-2 and HSV-1 and which represent modulators of transcription. (3) TATA homologies present 15-25 base pairs (bp) upstream of mRNA 5' termini. (4) a 137bp direct repeat in HSV-2 which contains sequence almost identical to the HSV-1 replication origin.

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Selected References

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

  1. Berk A. J., Sharp P. A. Spliced early mRNAs of simian virus 40. Proc Natl Acad Sci U S A. 1978 Mar;75(3):1274–1278. doi: 10.1073/pnas.75.3.1274. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Busslinger M., Portmann R., Irminger J. C., Birnstiel M. L. Ubiquitous and gene-specific regulatory 5' sequences in a sea urchin histone DNA clone coding for histone protein variants. Nucleic Acids Res. 1980 Mar 11;8(5):957–977. doi: 10.1093/nar/8.5.957. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Chartrand P., Stow N. D., Timbury M. C., Wilkie N. M. Physical mapping of paar mutations of herpes simplex virus type 1 and type 2 by intertypic marker rescue. J Virol. 1979 Aug;31(2):265–276. doi: 10.1128/jvi.31.2.265-276.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Clements J. B., Watson R. J., Wilkie N. M. Temporal regulation of herpes simplex virus type 1 transcription: location of transcripts on the viral genome. Cell. 1977 Sep;12(1):275–285. doi: 10.1016/0092-8674(77)90205-7. [DOI] [PubMed] [Google Scholar]
  5. Cordingley M. G., Campbell M. E., Preston C. M. Functional analysis of a herpes simplex virus type 1 promoter: identification of far-upstream regulatory sequences. Nucleic Acids Res. 1983 Apr 25;11(8):2347–2365. doi: 10.1093/nar/11.8.2347. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Costanzo F., Campadelli-Fiume G., Foa-Tomasi L., Cassai E. Evidence that herpes simplex virus DNA is transcribed by cellular RNA polymerase B. J Virol. 1977 Mar;21(3):996–1001. doi: 10.1128/jvi.21.3.996-1001.1977. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Davison A. J., Wilkie N. M. Location and orientation of homologous sequences in the genomes of five herpesviruses. J Gen Virol. 1983 Sep;64(Pt 9):1927–1942. doi: 10.1099/0022-1317-64-9-1927. [DOI] [PubMed] [Google Scholar]
  8. 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]
  9. Dierks P., van Ooyen A., Cochran M. D., Dobkin C., Reiser J., Weissmann C. Three regions upstream from the cap site are required for efficient and accurate transcription of the rabbit beta-globin gene in mouse 3T6 cells. Cell. 1983 Mar;32(3):695–706. doi: 10.1016/0092-8674(83)90055-7. [DOI] [PubMed] [Google Scholar]
  10. Donahue T. F., Daves R. S., Lucchini G., Fink G. R. A short nucleotide sequence required for regulation of HIS4 by the general control system of yeast. Cell. 1983 Jan;32(1):89–98. doi: 10.1016/0092-8674(83)90499-3. [DOI] [PubMed] [Google Scholar]
  11. Easton A. J., Clements J. B. Temporal regulation of herpes simplex virus type 2 transcription and characterization of virus immediate early mRNA's. Nucleic Acids Res. 1980 Jun 25;8(12):2627–2645. doi: 10.1093/nar/8.12.2627. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Edlund T., Normark S. Recombination between short DNA homologies causes tandem duplication. Nature. 1981 Jul 16;292(5820):269–271. doi: 10.1038/292269a0. [DOI] [PubMed] [Google Scholar]
  13. Enns R. E., Challberg M. D., Ahern K. G., Chow K. C., Mathews C. Z., Astell C. R., Pearson G. D. Mutational mapping of a cloned adenovirus origin. Gene. 1983 Sep;23(3):307–313. doi: 10.1016/0378-1119(83)90020-3. [DOI] [PubMed] [Google Scholar]
  14. Esparza J., Benyesh-Melnick B., Schaffer P. A. Intertypic complementation and recombination between temperature-sensitive mutants of herpes simplex virus types 1 and 2. Virology. 1976 Apr;70(2):372–384. doi: 10.1016/0042-6822(76)90279-8. [DOI] [PubMed] [Google Scholar]
  15. Everett R. D., Baty D., Chambon P. The repeated GC-rich motifs upstream from the TATA box are important elements of the SV40 early promoter. Nucleic Acids Res. 1983 Apr 25;11(8):2447–2464. doi: 10.1093/nar/11.8.2447. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Everett R. D. DNA sequence elements required for regulated expression of the HSV-1 glycoprotein D gene lie within 83 bp of the RNA capsites. Nucleic Acids Res. 1983 Oct 11;11(19):6647–6666. doi: 10.1093/nar/11.19.6647. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Fenwick M. L., Clark J. The effect of cycloheximide on the accumulation and stability of functional alpha-mRNA in cells infected with herpes simplex virus. J Gen Virol. 1983 Sep;64(Pt 9):1955–1963. doi: 10.1099/0022-1317-64-9-1955. [DOI] [PubMed] [Google Scholar]
  18. Gannon F., O'Hare K., Perrin F., LePennec J. P., Benoist C., Cochet M., Breathnach R., Royal A., Garapin A., Cami B. Organisation and sequences at the 5' end of a cloned complete ovalbumin gene. Nature. 1979 Mar 29;278(5703):428–434. doi: 10.1038/278428a0. [DOI] [PubMed] [Google Scholar]
  19. Grez M., Land H., Giesecke K., Schütz G., Jung A., Sippel A. E. Multiple mRNAs are generated from the chicken lysozyme gene. Cell. 1981 Sep;25(3):743–752. doi: 10.1016/0092-8674(81)90182-3. [DOI] [PubMed] [Google Scholar]
  20. Heintz N., Zernik M., Roeder R. G. The structure of the human histone genes: clustered but not tandemly repeated. Cell. 1981 Jun;24(3):661–668. doi: 10.1016/0092-8674(81)90092-1. [DOI] [PubMed] [Google Scholar]
  21. Hen R., Sassone-Corsi P., Corden J., Gaub M. P., Chambon P. Sequences upstream from the T-A-T-A box are required in vivo and in vitro for efficient transcription from the adenovirus serotype 2 major late promoter. Proc Natl Acad Sci U S A. 1982 Dec;79(23):7132–7136. doi: 10.1073/pnas.79.23.7132. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Hipskind R. A., Clarkson S. G. 5'-flanking sequences that inhibit in vitro transcription of a xenopus laevis tRNA gene. Cell. 1983 Oct;34(3):881–890. doi: 10.1016/0092-8674(83)90545-7. [DOI] [PubMed] [Google Scholar]
  23. Hudson P., Haley J., Cronk M., Shine J., Niall H. Molecular cloning and characterization of cDNA sequences coding for rat relaxin. Nature. 1981 May 14;291(5811):127–131. doi: 10.1038/291127a0. [DOI] [PubMed] [Google Scholar]
  24. Katinka M., Vasseur M., Montreau N., Yaniv M., Blangy D. Polyoma DNA sequences involved in control of viral gene expression in murine embryonal carcinoma cells. Nature. 1981 Apr 23;290(5808):720–722. doi: 10.1038/290720a0. [DOI] [PubMed] [Google Scholar]
  25. Kouzarides T., Bankier A. T., Barrell B. G. Nucleotide sequence of the transforming region of human cytomegalovirus. Mol Biol Med. 1983 Jul;1(1):47–58. [PubMed] [Google Scholar]
  26. Kozak M. Possible role of flanking nucleotides in recognition of the AUG initiator codon by eukaryotic ribosomes. Nucleic Acids Res. 1981 Oct 24;9(20):5233–5252. doi: 10.1093/nar/9.20.5233. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Luthman H., Nilsson M. G., Magnusson G. Non-contiguous segments of the polyoma genome required in cis for DNA replication. J Mol Biol. 1982 Nov 15;161(4):533–550. doi: 10.1016/0022-2836(82)90406-5. [DOI] [PubMed] [Google Scholar]
  28. Mackem S., Roizman B. Differentiation between alpha promoter and regulator regions of herpes simplex virus 1: the functional domains and sequence of a movable alpha regulator. Proc Natl Acad Sci U S A. 1982 Aug;79(16):4917–4921. doi: 10.1073/pnas.79.16.4917. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Mackem S., Roizman B. Structural features of the herpes simplex virus alpha gene 4, 0, and 27 promoter-regulatory sequences which confer alpha regulation on chimeric thymidine kinase genes. J Virol. 1982 Dec;44(3):939–949. doi: 10.1128/jvi.44.3.939-949.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
  31. McKnight S. L., Kingsbury R. Transcriptional control signals of a eukaryotic protein-coding gene. Science. 1982 Jul 23;217(4557):316–324. doi: 10.1126/science.6283634. [DOI] [PubMed] [Google Scholar]
  32. McLauchlan J., Clements J. B. DNA sequence homology between two co-linear loci on the HSV genome which have different transforming abilities. EMBO J. 1983;2(11):1953–1961. doi: 10.1002/j.1460-2075.1983.tb01684.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Murchie M. J., McGeoch D. J. DNA sequence analysis of an immediate-early gene region of the herpes simplex virus type 1 genome (map coordinates 0.950 to 0.978). J Gen Virol. 1982 Sep;62(Pt 1):1–15. doi: 10.1099/0022-1317-62-1-1. [DOI] [PubMed] [Google Scholar]
  34. Notarianni E. L., Preston C. M. Activation of cellular stress protein genes by herpes simplex virus temperature-sensitive mutants which overproduce immediate early polypeptides. Virology. 1982 Nov;123(1):113–122. doi: 10.1016/0042-6822(82)90299-9. [DOI] [PubMed] [Google Scholar]
  35. Omer C. A., Pogue-Geile K., Guntaka R., Staskus K. A., Faras A. J. Involvement of directly repeated sequences in the generation of deletions of the avian sarcoma virus src gene. J Virol. 1983 Aug;47(2):380–382. doi: 10.1128/jvi.47.2.380-382.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Pelham H. R. A regulatory upstream promoter element in the Drosophila hsp 70 heat-shock gene. Cell. 1982 Sep;30(2):517–528. doi: 10.1016/0092-8674(82)90249-5. [DOI] [PubMed] [Google Scholar]
  37. Pelham H. R., Bienz M. A synthetic heat-shock promoter element confers heat-inducibility on the herpes simplex virus thymidine kinase gene. EMBO J. 1982;1(11):1473–1477. doi: 10.1002/j.1460-2075.1982.tb01340.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Post L. E., Mackem S., Roizman B. Regulation of alpha genes of herpes simplex virus: expression of chimeric genes produced by fusion of thymidine kinase with alpha gene promoters. Cell. 1981 May;24(2):555–565. doi: 10.1016/0092-8674(81)90346-9. [DOI] [PubMed] [Google Scholar]
  39. Sheldrick P., Berthelot N. Inverted repetitions in the chromosome of herpes simplex virus. Cold Spring Harb Symp Quant Biol. 1975;39(Pt 2):667–678. doi: 10.1101/sqb.1974.039.01.080. [DOI] [PubMed] [Google Scholar]
  40. Stillman B. W., Topp W. C., Engler J. A. Conserved sequences at the origin of adenovirus DNA replication. J Virol. 1982 Nov;44(2):530–537. doi: 10.1128/jvi.44.2.530-537.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Stow N. D., McMonagle E. C. Characterization of the TRS/IRS origin of DNA replication of herpes simplex virus type 1. Virology. 1983 Oct 30;130(2):427–438. doi: 10.1016/0042-6822(83)90097-1. [DOI] [PubMed] [Google Scholar]
  42. Stow N. D., Wilkie N. M. Physical mapping of temperature-sensitive mutations of herpes simplex virus type 1 by intertypic marker rescue. Virology. 1978 Oct 1;90(1):1–11. doi: 10.1016/0042-6822(78)90327-6. [DOI] [PubMed] [Google Scholar]
  43. Watson R. J., Clements J. B. A herpes simplex virus type 1 function continuously required for early and late virus RNA synthesis. Nature. 1980 May 29;285(5763):329–330. doi: 10.1038/285329a0. [DOI] [PubMed] [Google Scholar]
  44. Watson R. J., Vande Woude G. F. DNA sequence of an immediate-early gene (IEmRNA-5) of herpes simplex virus type I. Nucleic Acids Res. 1982 Feb 11;10(3):979–991. doi: 10.1093/nar/10.3.979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Weaver R. F., Weissmann C. Mapping of RNA by a modification of the Berk-Sharp procedure: the 5' termini of 15 S beta-globin mRNA precursor and mature 10 s beta-globin mRNA have identical map coordinates. Nucleic Acids Res. 1979 Nov 10;7(5):1175–1193. doi: 10.1093/nar/7.5.1175. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Weiher H., König M., Gruss P. Multiple point mutations affecting the simian virus 40 enhancer. Science. 1983 Feb 11;219(4585):626–631. doi: 10.1126/science.6297005. [DOI] [PubMed] [Google Scholar]
  47. Whitton J. L., Rixon F. J., Easton A. J., Clements J. B. Immediate-early mRNA-2 of herpes simplex viruses types 1 and 2 is unspliced: conserved sequences around the 5' and 3' termini correspond to transcription regulatory signals. Nucleic Acids Res. 1983 Sep 24;11(18):6271–6287. doi: 10.1093/nar/11.18.6271. [DOI] [PMC free article] [PubMed] [Google Scholar]

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