Skip to main content
PMC home page
The Plant Cell logoLink to The Plant Cell
. 1995 Oct;7(10):1681–1689. doi: 10.1105/tpc.7.10.1681

TATA box and initiator functions in the accurate transcription of a plant minimal promoter in vitro.

Q Zhu 1, T Dabi 1, C Lamb 1
PMCID: PMC161029  PMID: 7580258

Abstract

The functional architecture of the proximal region of a rice phenylalanine ammonia-lyase (PAL) promoter was analyzed by transcription of PAL-beta-glucuronidase (GUS) templates by whole-cell extracts of rice cell suspension cultures. The promoter 5' truncated to position -35 was sufficient for accurate initiation of basal transcription. Substitution of the TATTTAA sequence between positions -35 and -28 with GCGGGTT or 2-bp substitutions to give TCGTTAA and TATGGAA inactivated the minimal promoter. Moreover, the function of the TATTTAA sequence was dependent on its position relative to the initiation site; hence, this element is an authentic TATA box essential for RNA polymerase II-dependent transcription. Substitutions in the TCCAAG initiator cis element (-3 to +3) at the -1 (C to A or G) and +1 (A to C or T) residues caused inaccurate initiation, whereas mutations at the other residues of this conserved element or sequence substitutions between the TATA box and initiator had little effect. TATA box and initiator functions were confirmed by analysis of the effects of promoter mutations on expression in stably transformed rice cell suspensions and plants. We concluded that the proximal region of the PAL promoter has a simple functional architecture involving a TATA box appropriately positioned upstream of the initiator. Transcription of derivatives of such minimal promoters by highly active cell extracts should allow molecular analysis of functional interactions between specific cis elements and cognate trans factors.

Full Text

The Full Text of this article is available as a PDF (3.0 MB).

Selected References

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

  1. Aso T., Conaway J. W., Conaway R. C. Role of core promoter structure in assembly of the RNA polymerase II preinitiation complex. A common pathway for formation of preinitiation intermediates at many TATA and TATA-less promoters. J Biol Chem. 1994 Oct 21;269(42):26575–26583. [PubMed] [Google Scholar]
  2. Aviv H., Leder P. Purification of biologically active globin messenger RNA by chromatography on oligothymidylic acid-cellulose. Proc Natl Acad Sci U S A. 1972 Jun;69(6):1408–1412. doi: 10.1073/pnas.69.6.1408. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Breathnach R., Chambon P. Organization and expression of eucaryotic split genes coding for proteins. Annu Rev Biochem. 1981;50:349–383. doi: 10.1146/annurev.bi.50.070181.002025. [DOI] [PubMed] [Google Scholar]
  4. Brunelle A. N., Chua N. H. Transcription regulatory proteins in higher plants. Curr Opin Genet Dev. 1993 Apr;3(2):254–258. doi: 10.1016/0959-437x(93)90031-j. [DOI] [PubMed] [Google Scholar]
  5. Buratowski S. The basics of basal transcription by RNA polymerase II. Cell. 1994 Apr 8;77(1):1–3. doi: 10.1016/0092-8674(94)90226-7. [DOI] [PubMed] [Google Scholar]
  6. Chen Z. L., Schuler M. A., Beachy R. N. Functional analysis of regulatory elements in a plant embryo-specific gene. Proc Natl Acad Sci U S A. 1986 Nov;83(22):8560–8564. doi: 10.1073/pnas.83.22.8560. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. 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]
  8. Gasch A., Hoffmann A., Horikoshi M., Roeder R. G., Chua N. H. Arabidopsis thaliana contains two genes for TFIID. Nature. 1990 Jul 26;346(6282):390–394. doi: 10.1038/346390a0. [DOI] [PubMed] [Google Scholar]
  9. Goldberg R. B., Barker S. J., Perez-Grau L. Regulation of gene expression during plant embryogenesis. Cell. 1989 Jan 27;56(2):149–160. doi: 10.1016/0092-8674(89)90888-x. [DOI] [PubMed] [Google Scholar]
  10. Goodrich J. A., Tjian R. Transcription factors IIE and IIH and ATP hydrolysis direct promoter clearance by RNA polymerase II. Cell. 1994 Apr 8;77(1):145–156. doi: 10.1016/0092-8674(94)90242-9. [DOI] [PubMed] [Google Scholar]
  11. Grayson J., Williams R. S., Yu Y. T., Bassel-Duby R. Synergistic interactions between heterologous upstream activation elements and specific TATA sequences in a muscle-specific promoter. Mol Cell Biol. 1995 Apr;15(4):1870–1878. doi: 10.1128/mcb.15.4.1870. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Holstege F. C., Tantin D., Carey M., van der Vliet P. C., Timmers H. T. The requirement for the basal transcription factor IIE is determined by the helical stability of promoter DNA. EMBO J. 1995 Feb 15;14(4):810–819. doi: 10.1002/j.1460-2075.1995.tb07059.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Katagiri F., Chua N. H. Plant transcription factors: present knowledge and future challenges. Trends Genet. 1992 Jan;8(1):22–27. doi: 10.1016/0168-9525(92)90020-5. [DOI] [PubMed] [Google Scholar]
  14. Kloeckener-Gruissem B., Vogel J. M., Freeling M. The TATA box promoter region of maize Adh1 affects its organ-specific expression. EMBO J. 1992 Jan;11(1):157–166. doi: 10.1002/j.1460-2075.1992.tb05038.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Li Y., Flanagan P. M., Tschochner H., Kornberg R. D. RNA polymerase II initiation factor interactions and transcription start site selection. Science. 1994 Feb 11;263(5148):805–807. doi: 10.1126/science.8303296. [DOI] [PubMed] [Google Scholar]
  16. Lin Y. S., Green M. R. Mechanism of action of an acidic transcriptional activator in vitro. Cell. 1991 Mar 8;64(5):971–981. doi: 10.1016/0092-8674(91)90321-o. [DOI] [PubMed] [Google Scholar]
  17. Martinez E., Chiang C. M., Ge H., Roeder R. G. TATA-binding protein-associated factor(s) in TFIID function through the initiator to direct basal transcription from a TATA-less class II promoter. EMBO J. 1994 Jul 1;13(13):3115–3126. doi: 10.1002/j.1460-2075.1994.tb06610.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Means A. L., Farnham P. J. Transcription initiation from the dihydrofolate reductase promoter is positioned by HIP1 binding at the initiation site. Mol Cell Biol. 1990 Feb;10(2):653–661. doi: 10.1128/mcb.10.2.653. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Minami E., Ozeki Y., Matsuoka M., Koizuka N., Tanaka Y. Structure and some characterization of the gene for phenylalanine ammonia-lyase from rice plants. Eur J Biochem. 1989 Oct 20;185(1):19–25. doi: 10.1111/j.1432-1033.1989.tb15075.x. [DOI] [PubMed] [Google Scholar]
  20. Minami E., Tanaka Y. Nucleotide sequence of the gene for phenylalanine ammonia-lyase of rice and its deduced amino acid sequence. Biochim Biophys Acta. 1993 Jan 23;1171(3):321–322. doi: 10.1016/0167-4781(93)90075-o. [DOI] [PubMed] [Google Scholar]
  21. Mukumoto F., Hirose S., Imaseki H., Yamazaki K. DNA sequence requirement of a TATA element-binding protein from Arabidopsis for transcription in vitro. Plant Mol Biol. 1993 Dec;23(5):995–1003. doi: 10.1007/BF00021814. [DOI] [PubMed] [Google Scholar]
  22. O'Shea-Greenfield A., Smale S. T. Roles of TATA and initiator elements in determining the start site location and direction of RNA polymerase II transcription. J Biol Chem. 1992 Jan 15;267(2):1391–1402. [PubMed] [Google Scholar]
  23. 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]
  24. Schaeffer L., Roy R., Humbert S., Moncollin V., Vermeulen W., Hoeijmakers J. H., Chambon P., Egly J. M. DNA repair helicase: a component of BTF2 (TFIIH) basic transcription factor. Science. 1993 Apr 2;260(5104):58–63. doi: 10.1126/science.8465201. [DOI] [PubMed] [Google Scholar]
  25. 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]
  26. Singer V. L., Wobbe C. R., Struhl K. A wide variety of DNA sequences can functionally replace a yeast TATA element for transcriptional activation. Genes Dev. 1990 Apr;4(4):636–645. doi: 10.1101/gad.4.4.636. [DOI] [PubMed] [Google Scholar]
  27. 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]
  28. Struhl K. Promoters, activator proteins, and the mechanism of transcriptional initiation in yeast. Cell. 1987 May 8;49(3):295–297. doi: 10.1016/0092-8674(87)90277-7. [DOI] [PubMed] [Google Scholar]
  29. Tjian R., Maniatis T. Transcriptional activation: a complex puzzle with few easy pieces. Cell. 1994 Apr 8;77(1):5–8. doi: 10.1016/0092-8674(94)90227-5. [DOI] [PubMed] [Google Scholar]
  30. Weis L., Reinberg D. Transcription by RNA polymerase II: initiator-directed formation of transcription-competent complexes. FASEB J. 1992 Nov;6(14):3300–3309. doi: 10.1096/fasebj.6.14.1426767. [DOI] [PubMed] [Google Scholar]
  31. Zenzie-Gregory B., O'Shea-Greenfield A., Smale S. T. Similar mechanisms for transcription initiation mediated through a TATA box or an initiator element. J Biol Chem. 1992 Feb 5;267(4):2823–2830. [PubMed] [Google Scholar]
  32. Zhu Q., Chappell J., Hedrick S. A., Lamb C. Accurate in vitro transcription from circularized plasmid templates by plant whole cell extracts. Plant J. 1995 Jun;7(6):1021–1030. doi: 10.1046/j.1365-313x.1995.07061021.x. [DOI] [PubMed] [Google Scholar]

Articles from The Plant Cell are provided here courtesy of Oxford University Press

RESOURCES