Skip to main content
PMC home page
Journal of Virology logoLink to Journal of Virology
. 1997 Jan;71(1):102–109. doi: 10.1128/jvi.71.1.102-109.1997

The initiator element of the adenovirus major late promoter has an important role in transcription initiation in vivo.

H Lu 1, M D Reach 1, E Minaya 1, C S Young 1
PMCID: PMC191029  PMID: 8985328

Abstract

Previous results showed that the structure and function of the adenovirus major late promoter (MLP) can be analyzed genetically in its correct location, despite its essential role in the viral life cycle. This genetic approach was extended to investigate the in vivo role of the initiator (INR), a transcriptional element that surrounds the start site of transcription. The analysis was designed to investigate if the INR is an alternative basal element to the canonical TATA box of the MLP, its relative importance in the functioning of the promoter, and if its function was affected by upstream activating elements. Accordingly, two different mutations in the INR were created and tested in the genome, either by themselves or together with mutations in the TATA box or one of the two upstream activating elements, the upstream promoter element (UPE) and the inverted CAAT box. The mutant viruses were examined first in one-step growth experiments, and then levels of late mRNA accumulation were measured by primer extension, transcription initiation was assayed in isolated nuclei, and viral DNA accumulation was determined by Southern hybridization. Neither mutation in the INR alone had any discernible phenotypic effects but when coupled to a phenotypically silent mutation in the TATA box gave rise to viruses with growth defects that were attributable to a significantly lowered rate of transcription initiation from the MLP. These results suggest that the INR plays a role in vivo and can act as an alternative basal element in the absence of a functioning TATA box. A virus with mutations in both the INR and the UPE, although viable, likewise had a severe deficiency in transcription, suggesting that the function of the INR is affected by that of the UPE. This contrasts with the previous report that a TATA box-UPE double mutation is not recoverable in virus. In addition, the virus with mutations in both the INR and the inverted CAAT box was phenotypically wild type, unlike the previously described TATA box-CAAT box double mutant, which had a severe transcription deficiency. Taken together, the present and previous genetic results can be interpreted as evidence that in the MLP, the TATA box and the UPE are the more important of the two basal and activating elements, respectively, but that the INR and CAAT can function in transcription initiation. We consider the role of the INR in the formation of the preinitiation complex and speculate on possible protein-protein interactions.

Full Text

The Full Text of this article is available as a PDF (304.7 KB).

Selected References

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

  1. Bendall A. J., Molloy P. L. Base preferences for DNA binding by the bHLH-Zip protein USF: effects of MgCl2 on specificity and comparison with binding of Myc family members. Nucleic Acids Res. 1994 Jul 25;22(14):2801–2810. doi: 10.1093/nar/22.14.2801. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Brunet L. J., Babiss L. E., Young C. S., Mills D. R. Mutations in the adenovirus major late promoter: effects on viability and transcription during infection. Mol Cell Biol. 1987 Mar;7(3):1091–1100. doi: 10.1128/mcb.7.3.1091. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bucher P. Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. J Mol Biol. 1990 Apr 20;212(4):563–578. doi: 10.1016/0022-2836(90)90223-9. [DOI] [PubMed] [Google Scholar]
  4. Burley S. K. Picking up the TAB. Nature. 1996 May 9;381(6578):112–113. doi: 10.1038/381112a0. [DOI] [PubMed] [Google Scholar]
  5. Carcamo J., Buckbinder L., Reinberg D. The initiator directs the assembly of a transcription factor IID-dependent transcription complex. Proc Natl Acad Sci U S A. 1991 Sep 15;88(18):8052–8056. doi: 10.1073/pnas.88.18.8052. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Carcamo J., Maldonado E., Cortes P., Ahn M. H., Ha I., Kasai Y., Flint J., Reinberg D. A TATA-like sequence located downstream of the transcription initiation site is required for expression of an RNA polymerase II transcribed gene. Genes Dev. 1990 Sep;4(9):1611–1622. doi: 10.1101/gad.4.9.1611. [DOI] [PubMed] [Google Scholar]
  7. Chang C., Gralla J. D. Properties of initiator-associated transcription mediated by GAL4-VP16. Mol Cell Biol. 1993 Dec;13(12):7469–7475. doi: 10.1128/mcb.13.12.7469. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Chen J. L., Attardi L. D., Verrijzer C. P., Yokomori K., Tjian R. Assembly of recombinant TFIID reveals differential coactivator requirements for distinct transcriptional activators. Cell. 1994 Oct 7;79(1):93–105. doi: 10.1016/0092-8674(94)90403-0. [DOI] [PubMed] [Google Scholar]
  9. Chodosh L. A., Baldwin A. S., Carthew R. W., Sharp P. A. Human CCAAT-binding proteins have heterologous subunits. Cell. 1988 Apr 8;53(1):11–24. doi: 10.1016/0092-8674(88)90483-7. [DOI] [PubMed] [Google Scholar]
  10. Chodosh L. A., Carthew R. W., Sharp P. A. A single polypeptide possesses the binding and transcription activities of the adenovirus major late transcription factor. Mol Cell Biol. 1986 Dec;6(12):4723–4733. doi: 10.1128/mcb.6.12.4723. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Chomczynski P., Sacchi N. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem. 1987 Apr;162(1):156–159. doi: 10.1006/abio.1987.9999. [DOI] [PubMed] [Google Scholar]
  12. Colgan J., Manley J. L. Cooperation between core promoter elements influences transcriptional activity in vivo. Proc Natl Acad Sci U S A. 1995 Mar 14;92(6):1955–1959. doi: 10.1073/pnas.92.6.1955. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Conaway R. C., Conaway J. W. General initiation factors for RNA polymerase II. Annu Rev Biochem. 1993;62:161–190. doi: 10.1146/annurev.bi.62.070193.001113. [DOI] [PubMed] [Google Scholar]
  14. Concino M. F., Lee R. F., Merryweather J. P., Weinmann R. The adenovirus major late promoter TATA box and initiation site are both necessary for transcription in vitro. Nucleic Acids Res. 1984 Oct 11;12(19):7423–7433. doi: 10.1093/nar/12.19.7423. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Du H., Roy A. L., Roeder R. G. Human transcription factor USF stimulates transcription through the initiator elements of the HIV-1 and the Ad-ML promoters. EMBO J. 1993 Feb;12(2):501–511. doi: 10.1002/j.1460-2075.1993.tb05682.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Emami K. H., Navarre W. W., Smale S. T. Core promoter specificities of the Sp1 and VP16 transcriptional activation domains. Mol Cell Biol. 1995 Nov;15(11):5906–5916. doi: 10.1128/mcb.15.11.5906. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Fort P., Marty L., Piechaczyk M., el Sabrouty S., Dani C., Jeanteur P., Blanchard J. M. Various rat adult tissues express only one major mRNA species from the glyceraldehyde-3-phosphate-dehydrogenase multigenic family. Nucleic Acids Res. 1985 Mar 11;13(5):1431–1442. doi: 10.1093/nar/13.5.1431. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Garfinkel S., Thompson J. A., Jacob W. F., Cohen R., Safer B. Identification and characterization of an adenovirus 2 major late promoter CAP sequence DNA-binding protein. J Biol Chem. 1990 Jun 25;265(18):10309–10319. [PubMed] [Google Scholar]
  19. Geiger J. H., Hahn S., Lee S., Sigler P. B. Crystal structure of the yeast TFIIA/TBP/DNA complex. Science. 1996 May 10;272(5263):830–836. doi: 10.1126/science.272.5263.830. [DOI] [PubMed] [Google Scholar]
  20. Jacobson R. H., Tjian R. Transcription factor IIA: a structure with multiple functions. Science. 1996 May 10;272(5263):827–828. doi: 10.1126/science.272.5263.827. [DOI] [PubMed] [Google Scholar]
  21. Javahery R., Khachi A., Lo K., Zenzie-Gregory B., Smale S. T. DNA sequence requirements for transcriptional initiator activity in mammalian cells. Mol Cell Biol. 1994 Jan;14(1):116–127. doi: 10.1128/mcb.14.1.116. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Kasai Y., Chen H., Flint S. J. Anatomy of an unusual RNA polymerase II promoter containing a downstream TATA element. Mol Cell Biol. 1992 Jun;12(6):2884–2897. doi: 10.1128/mcb.12.6.2884. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Kaufmann J., Verrijzer C. P., Shao J., Smale S. T. CIF, an essential cofactor for TFIID-dependent initiator function. Genes Dev. 1996 Apr 1;10(7):873–886. doi: 10.1101/gad.10.7.873. [DOI] [PubMed] [Google Scholar]
  24. Kim J. L., Nikolov D. B., Burley S. K. Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature. 1993 Oct 7;365(6446):520–527. doi: 10.1038/365520a0. [DOI] [PubMed] [Google Scholar]
  25. Kokubo T., Takada R., Yamashita S., Gong D. W., Roeder R. G., Horikoshi M., Nakatani Y. Identification of TFIID components required for transcriptional activation by upstream stimulatory factor. J Biol Chem. 1993 Aug 15;268(23):17554–17558. [PubMed] [Google Scholar]
  26. Kunkel T. A. Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc Natl Acad Sci U S A. 1985 Jan;82(2):488–492. doi: 10.1073/pnas.82.2.488. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Lawrence W. C., Ginsberg H. S. Intracellular uncoating of type 5 adenovirus deoxyribonucleic acid. J Virol. 1967 Oct;1(5):851–867. doi: 10.1128/jvi.1.5.851-867.1967. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Lee R. F., Concino M. F., Weinmann R. Genetic profile of the transcriptional signals from the adenovirus major late promoter. Virology. 1988 Jul;165(1):51–56. doi: 10.1016/0042-6822(88)90657-5. [DOI] [PubMed] [Google Scholar]
  29. Manzano-Winkler B., Novina C. D., Roy A. L. TFII is required for transcription of the naturally TATA-less but initiator-containing Vbeta promoter. J Biol Chem. 1996 May 17;271(20):12076–12081. doi: 10.1074/jbc.271.20.12076. [DOI] [PubMed] [Google Scholar]
  30. Miyamoto N. G., Moncollin V., Egly J. M., Chambon P. Specific interaction between a transcription factor and the upstream element of the adenovirus-2 major late promoter. EMBO J. 1985 Dec 16;4(13A):3563–3570. doi: 10.1002/j.1460-2075.1985.tb04118.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Nikolov D. B., Chen H., Halay E. D., Hoffman A., Roeder R. G., Burley S. K. Crystal structure of a human TATA box-binding protein/TATA element complex. Proc Natl Acad Sci U S A. 1996 May 14;93(10):4862–4867. doi: 10.1073/pnas.93.10.4862. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Nikolov D. B., Chen H., Halay E. D., Usheva A. A., Hisatake K., Lee D. K., Roeder R. G., Burley S. K. Crystal structure of a TFIIB-TBP-TATA-element ternary complex. Nature. 1995 Sep 14;377(6545):119–128. doi: 10.1038/377119a0. [DOI] [PubMed] [Google Scholar]
  33. Reach M., Babiss L. E., Young C. S. The upstream factor-binding site is not essential for activation of transcription from the adenovirus major late promoter. J Virol. 1990 Dec;64(12):5851–5860. doi: 10.1128/jvi.64.12.5851-5860.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Reach M., Xu L. X., Young C. S. Transcription from the adenovirus major late promoter uses redundant activating elements. EMBO J. 1991 Nov;10(11):3439–3446. doi: 10.1002/j.1460-2075.1991.tb04908.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Roy A. L., Malik S., Meisterernst M., Roeder R. G. An alternative pathway for transcription initiation involving TFII-I. Nature. 1993 Sep 23;365(6444):355–359. doi: 10.1038/365355a0. [DOI] [PubMed] [Google Scholar]
  36. Roy A. L., Meisterernst M., Pognonec P., Roeder R. G. Cooperative interaction of an initiator-binding transcription initiation factor and the helix-loop-helix activator USF. Nature. 1991 Nov 21;354(6350):245–248. doi: 10.1038/354245a0. [DOI] [PubMed] [Google Scholar]
  37. Safer B., Cohen R. B., Garfinkel S., Thompson J. A. DNA affinity labeling of adenovirus type 2 upstream promoter sequence-binding factors identifies two distinct proteins. Mol Cell Biol. 1988 Jan;8(1):105–113. doi: 10.1128/mcb.8.1.105. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Sawadogo M., Roeder R. G. Interaction of a gene-specific transcription factor with the adenovirus major late promoter upstream of the TATA box region. Cell. 1985 Nov;43(1):165–175. doi: 10.1016/0092-8674(85)90021-2. [DOI] [PubMed] [Google Scholar]
  39. Seto E., Shi Y., Shenk T. YY1 is an initiator sequence-binding protein that directs and activates transcription in vitro. Nature. 1991 Nov 21;354(6350):241–245. doi: 10.1038/354241a0. [DOI] [PubMed] [Google Scholar]
  40. Smale S. T., Baltimore D. The "initiator" as a transcription control element. Cell. 1989 Apr 7;57(1):103–113. doi: 10.1016/0092-8674(89)90176-1. [DOI] [PubMed] [Google Scholar]
  41. Smale S. T., Schmidt M. C., Berk A. J., Baltimore D. Transcriptional activation by Sp1 as directed through TATA or initiator: specific requirement for mammalian transcription factor IID. Proc Natl Acad Sci U S A. 1990 Jun;87(12):4509–4513. doi: 10.1073/pnas.87.12.4509. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Starr D. B., Hawley D. K. TFIID binds in the minor groove of the TATA box. Cell. 1991 Dec 20;67(6):1231–1240. doi: 10.1016/0092-8674(91)90299-e. [DOI] [PubMed] [Google Scholar]
  43. Swaminathan S., Thimmapaya B. Transactivation of adenovirus E2-early promoter by E1A and E4 6/7 in the context of viral chromosome. J Mol Biol. 1996 May 24;258(5):736–746. doi: 10.1006/jmbi.1996.0283. [DOI] [PubMed] [Google Scholar]
  44. Tan S., Hunziker Y., Sargent D. F., Richmond T. J. Crystal structure of a yeast TFIIA/TBP/DNA complex. Nature. 1996 May 9;381(6578):127–151. doi: 10.1038/381127a0. [DOI] [PubMed] [Google Scholar]
  45. Thomas G. P., Mathews M. B. DNA replication and the early to late transition in adenovirus infection. Cell. 1980 Nov;22(2 Pt 2):523–533. doi: 10.1016/0092-8674(80)90362-1. [DOI] [PubMed] [Google Scholar]
  46. Verrijzer C. P., Chen J. L., Yokomori K., Tjian R. Binding of TAFs to core elements directs promoter selectivity by RNA polymerase II. Cell. 1995 Jun 30;81(7):1115–1125. doi: 10.1016/s0092-8674(05)80016-9. [DOI] [PubMed] [Google Scholar]
  47. Verrijzer C. P., Yokomori K., Chen J. L., Tjian R. Drosophila TAFII150: similarity to yeast gene TSM-1 and specific binding to core promoter DNA. Science. 1994 May 13;264(5161):933–941. doi: 10.1126/science.8178153. [DOI] [PubMed] [Google Scholar]
  48. Volkert F. C., Munz P. L., Young C. S. A genetic investigation of the mechanism of adenovirus marker rescue. Virology. 1989 Nov;173(1):77–88. doi: 10.1016/0042-6822(89)90223-7. [DOI] [PubMed] [Google Scholar]
  49. Volkert F. C., Young C. S. The genetic analysis of recombination using adenovirus overlapping terminal DNA fragments. Virology. 1983 Feb;125(1):175–193. doi: 10.1016/0042-6822(83)90072-7. [DOI] [PubMed] [Google Scholar]
  50. Yang U. C., Huang W., Flint S. J. mRNA export correlates with activation of transcription in human subgroup C adenovirus-infected cells. J Virol. 1996 Jun;70(6):4071–4080. doi: 10.1128/jvi.70.6.4071-4080.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Zawel L., Reinberg D. Advances in RNA polymerase II transcription. Curr Opin Cell Biol. 1992 Jun;4(3):488–495. doi: 10.1016/0955-0674(92)90016-6. [DOI] [PubMed] [Google Scholar]
  52. Zenzie-Gregory B., Khachi A., Garraway I. P., Smale S. T. Mechanism of initiator-mediated transcription: evidence for a functional interaction between the TATA-binding protein and DNA in the absence of a specific recognition sequence. Mol Cell Biol. 1993 Jul;13(7):3841–3849. doi: 10.1128/mcb.13.7.3841. [DOI] [PMC free article] [PubMed] [Google Scholar]

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

RESOURCES