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. 1992 Apr;11(4):1275–1289. doi: 10.1002/j.1460-2075.1992.tb05171.x

DNA binding site preferences and transcriptional activation properties of the Arabidopsis transcription factor GBF1.

U Schindler 1, W Terzaghi 1, H Beckmann 1, T Kadesch 1, A R Cashmore 1
PMCID: PMC556575  PMID: 1563344

Abstract

The G-box is a cis-acting element found within the promoters of many plant genes where it mediates expression in response to a variety of different stimuli. This palindromic DNA motif (CCACGTGG) is composed of two identical half sites, the base pairs of which we have numbered -4 to +4 (numbering from 5' to 3'). Both half sites are involved in the binding of the bZIP protein GBF1, a member of the GBF family of Arabidopsis thaliana. Here we demonstrate using the random binding site selection method that GBF1 interacts with, in addition to the palindromic G-box, other DNA motifs that fall into seven distinct groups. All groups share the ACGT core sequence, common to most DNA motifs bound by plant bZIP proteins so far characterized. Our studies demonstrate that a high affinity GBF1 binding site is further defined by the following two parameters: first, all sites contain a G residue at position +3 (as in ACGTG) and secondly, only certain base pair combinations are allowed at positions -4, -3 and +4. Two of the identified groups (TGACGTGG and TGACGTGT) contain the base pairs TG at positions -4 and -3 and hence resemble the binding sites of another class of plant bZIP proteins (TGACGT/C binding proteins). However, GBF1 only interacts with the TGACGT sequence if the two 3' distal nucleotides (positions +3 and +4) are occupied by GG or GT. These data define the differences between a G-box binding protein and TGACGT/C binding proteins. The N-terminal domain of GBF1 is defined by a high proline content. Such regions were also identified in proteins related to GBF1. We demonstrate that this N-terminal proline-rich domain of GBF1, when fused to a heterologous DNA binding domain, stimulates transcription in both plant protoplasts and mammalian cells. These extensive DNA binding studies and the characterization of the GBF1 activation domain will facilitate both the identification of regulatory elements and the in vivo function of GBF1.

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Selected References

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

  1. Abate C., Luk D., Gentz R., Rauscher F. J., 3rd, Curran T. Expression and purification of the leucine zipper and DNA-binding domains of Fos and Jun: both Fos and Jun contact DNA directly. Proc Natl Acad Sci U S A. 1990 Feb;87(3):1032–1036. doi: 10.1073/pnas.87.3.1032. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Beckmann H., Su L. K., Kadesch T. TFE3: a helix-loop-helix protein that activates transcription through the immunoglobulin enhancer muE3 motif. Genes Dev. 1990 Feb;4(2):167–179. doi: 10.1101/gad.4.2.167. [DOI] [PubMed] [Google Scholar]
  3. Blackwell T. K., Weintraub H. Differences and similarities in DNA-binding preferences of MyoD and E2A protein complexes revealed by binding site selection. Science. 1990 Nov 23;250(4984):1104–1110. doi: 10.1126/science.2174572. [DOI] [PubMed] [Google Scholar]
  4. Carey M., Lin Y. S., Green M. R., Ptashne M. A mechanism for synergistic activation of a mammalian gene by GAL4 derivatives. Nature. 1990 May 24;345(6273):361–364. doi: 10.1038/345361a0. [DOI] [PubMed] [Google Scholar]
  5. Castresana C., Garcia-Luque I., Alonso E., Malik V. S., Cashmore A. R. Both positive and negative regulatory elements mediate expression of a photoregulated CAB gene from Nicotiana plumbaginifolia. EMBO J. 1988 Jul;7(7):1929–1936. doi: 10.1002/j.1460-2075.1988.tb03030.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Courey A. J., Holtzman D. A., Jackson S. P., Tjian R. Synergistic activation by the glutamine-rich domains of human transcription factor Sp1. Cell. 1989 Dec 1;59(5):827–836. doi: 10.1016/0092-8674(89)90606-5. [DOI] [PubMed] [Google Scholar]
  7. DeLisle A. J., Ferl R. J. Characterization of the Arabidopsis Adh G-box binding factor. Plant Cell. 1990 Jun;2(6):547–557. doi: 10.1105/tpc.2.6.547. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Donald R. G., Cashmore A. R. Mutation of either G box or I box sequences profoundly affects expression from the Arabidopsis rbcS-1A promoter. EMBO J. 1990 Jun;9(6):1717–1726. doi: 10.1002/j.1460-2075.1990.tb08295.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Donald R. G., Schindler U., Batschauer A., Cashmore A. R. The plant G box promoter sequence activates transcription in Saccharomyces cerevisiae and is bound in vitro by a yeast activity similar to GBF, the plant G box binding factor. EMBO J. 1990 Jun;9(6):1727–1735. doi: 10.1002/j.1460-2075.1990.tb08296.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Ekker S. C., Young K. E., von Kessler D. P., Beachy P. A. Optimal DNA sequence recognition by the Ultrabithorax homeodomain of Drosophila. EMBO J. 1991 May;10(5):1179–1186. doi: 10.1002/j.1460-2075.1991.tb08058.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Fischer J. A., Giniger E., Maniatis T., Ptashne M. GAL4 activates transcription in Drosophila. Nature. 1988 Apr 28;332(6167):853–856. doi: 10.1038/332853a0. [DOI] [PubMed] [Google Scholar]
  12. Frankel A. D., Kim P. S. Modular structure of transcription factors: implications for gene regulation. Cell. 1991 May 31;65(5):717–719. doi: 10.1016/0092-8674(91)90378-c. [DOI] [PubMed] [Google Scholar]
  13. Gerster T., Balmaceda C. G., Roeder R. G. The cell type-specific octamer transcription factor OTF-2 has two domains required for the activation of transcription. EMBO J. 1990 May;9(5):1635–1643. doi: 10.1002/j.1460-2075.1990.tb08283.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Gregor P. D., Sawadogo M., Roeder R. G. The adenovirus major late transcription factor USF is a member of the helix-loop-helix group of regulatory proteins and binds to DNA as a dimer. Genes Dev. 1990 Oct;4(10):1730–1740. doi: 10.1101/gad.4.10.1730. [DOI] [PubMed] [Google Scholar]
  15. Gronemeyer H., Turcotte B., Quirin-Stricker C., Bocquel M. T., Meyer M. E., Krozowski Z., Jeltsch J. M., Lerouge T., Garnier J. M., Chambon P. The chicken progesterone receptor: sequence, expression and functional analysis. EMBO J. 1987 Dec 20;6(13):3985–3994. doi: 10.1002/j.1460-2075.1987.tb02741.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Guiltinan M. J., Marcotte W. R., Jr, Quatrano R. S. A plant leucine zipper protein that recognizes an abscisic acid response element. Science. 1990 Oct 12;250(4978):267–271. doi: 10.1126/science.2145628. [DOI] [PubMed] [Google Scholar]
  17. Hope I. A., Struhl K. Functional dissection of a eukaryotic transcriptional activator protein, GCN4 of yeast. Cell. 1986 Sep 12;46(6):885–894. doi: 10.1016/0092-8674(86)90070-x. [DOI] [PubMed] [Google Scholar]
  18. Hu J. C., O'Shea E. K., Kim P. S., Sauer R. T. Sequence requirements for coiled-coils: analysis with lambda repressor-GCN4 leucine zipper fusions. Science. 1990 Dec 7;250(4986):1400–1403. doi: 10.1126/science.2147779. [DOI] [PubMed] [Google Scholar]
  19. Johnson P. F., McKnight S. L. Eukaryotic transcriptional regulatory proteins. Annu Rev Biochem. 1989;58:799–839. doi: 10.1146/annurev.bi.58.070189.004055. [DOI] [PubMed] [Google Scholar]
  20. Jones N. C., Rigby P. W., Ziff E. B. Trans-acting protein factors and the regulation of eukaryotic transcription: lessons from studies on DNA tumor viruses. Genes Dev. 1988 Mar;2(3):267–281. doi: 10.1101/gad.2.3.267. [DOI] [PubMed] [Google Scholar]
  21. Kakidani H., Ptashne M. GAL4 activates gene expression in mammalian cells. Cell. 1988 Jan 29;52(2):161–167. doi: 10.1016/0092-8674(88)90504-1. [DOI] [PubMed] [Google Scholar]
  22. Katagiri F., Lam E., Chua N. H. Two tobacco DNA-binding proteins with homology to the nuclear factor CREB. Nature. 1989 Aug 31;340(6236):727–730. doi: 10.1038/340727a0. [DOI] [PubMed] [Google Scholar]
  23. Katagiri F., Yamazaki K., Horikoshi M., Roeder R. G., Chua N. H. A plant DNA-binding protein increases the number of active preinitiation complexes in a human in vitro transcription system. Genes Dev. 1990 Nov;4(11):1899–1909. doi: 10.1101/gad.4.11.1899. [DOI] [PubMed] [Google Scholar]
  24. Kumar V., Green S., Stack G., Berry M., Jin J. R., Chambon P. Functional domains of the human estrogen receptor. Cell. 1987 Dec 24;51(6):941–951. doi: 10.1016/0092-8674(87)90581-2. [DOI] [PubMed] [Google Scholar]
  25. Landschulz W. H., Johnson P. F., McKnight S. L. The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins. Science. 1988 Jun 24;240(4860):1759–1764. doi: 10.1126/science.3289117. [DOI] [PubMed] [Google Scholar]
  26. Latchman D. S. Eukaryotic transcription factors. Biochem J. 1990 Sep 1;270(2):281–289. doi: 10.1042/bj2700281. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Laughon A., Scott M. P. Sequence of a Drosophila segmentation gene: protein structure homology with DNA-binding proteins. Nature. 1984 Jul 5;310(5972):25–31. doi: 10.1038/310025a0. [DOI] [PubMed] [Google Scholar]
  28. Lee F., Hall C. V., Ringold G. M., Dobson D. E., Luh J., Jacob P. E. Functional analysis of the steroid hormone control region of mouse mammary tumor virus. Nucleic Acids Res. 1984 May 25;12(10):4191–4206. doi: 10.1093/nar/12.10.4191. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Lillie J. W., Green M. R. Transcription activation by the adenovirus E1a protein. Nature. 1989 Mar 2;338(6210):39–44. doi: 10.1038/338039a0. [DOI] [PubMed] [Google Scholar]
  30. Lin W., Odell J. T., Schreiner R. M. Soybean protoplast culture and direct gene uptake and expression by cultured soybean protoplasts. Plant Physiol. 1987 Jul;84(3):856–861. doi: 10.1104/pp.84.3.856. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Lohmer S., Maddaloni M., Motto M., Di Fonzo N., Hartings H., Salamini F., Thompson R. D. The maize regulatory locus Opaque-2 encodes a DNA-binding protein which activates the transcription of the b-32 gene. EMBO J. 1991 Mar;10(3):617–624. doi: 10.1002/j.1460-2075.1991.tb07989.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Ma J., Przibilla E., Hu J., Bogorad L., Ptashne M. Yeast activators stimulate plant gene expression. Nature. 1988 Aug 18;334(6183):631–633. doi: 10.1038/334631a0. [DOI] [PubMed] [Google Scholar]
  33. Ma J., Ptashne M. Deletion analysis of GAL4 defines two transcriptional activating segments. Cell. 1987 Mar 13;48(5):847–853. doi: 10.1016/0092-8674(87)90081-x. [DOI] [PubMed] [Google Scholar]
  34. 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]
  35. Mermod N., O'Neill E. A., Kelly T. J., Tjian R. The proline-rich transcriptional activator of CTF/NF-I is distinct from the replication and DNA binding domain. Cell. 1989 Aug 25;58(4):741–753. doi: 10.1016/0092-8674(89)90108-6. [DOI] [PubMed] [Google Scholar]
  36. Mitchell P. J., Tjian R. Transcriptional regulation in mammalian cells by sequence-specific DNA binding proteins. Science. 1989 Jul 28;245(4916):371–378. doi: 10.1126/science.2667136. [DOI] [PubMed] [Google Scholar]
  37. Müller-Immerglück M. M., Schaffner W., Matthias P. Transcription factor Oct-2A contains functionally redundant activating domains and works selectively from a promoter but not from a remote enhancer position in non-lymphoid (HeLa) cells. EMBO J. 1990 May;9(5):1625–1634. doi: 10.1002/j.1460-2075.1990.tb08282.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Oeda K., Salinas J., Chua N. H. A tobacco bZip transcription activator (TAF-1) binds to a G-box-like motif conserved in plant genes. EMBO J. 1991 Jul;10(7):1793–1802. doi: 10.1002/j.1460-2075.1991.tb07704.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Ptashne M. How eukaryotic transcriptional activators work. Nature. 1988 Oct 20;335(6192):683–689. doi: 10.1038/335683a0. [DOI] [PubMed] [Google Scholar]
  40. Ransone L. J., Wamsley P., Morley K. L., Verma I. M. Domain swapping reveals the modular nature of Fos, Jun, and CREB proteins. Mol Cell Biol. 1990 Sep;10(9):4565–4573. doi: 10.1128/mcb.10.9.4565. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Rasmussen R., Benvegnu D., O'Shea E. K., Kim P. S., Alber T. X-ray scattering indicates that the leucine zipper is a coiled coil. Proc Natl Acad Sci U S A. 1991 Jan 15;88(2):561–564. doi: 10.1073/pnas.88.2.561. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Rogers S. M., Ogren W. L., Widholm J. M. Photosynthetic characteristics of a photoautotrophic cell suspension culture of soybean. Plant Physiol. 1987 Aug;84(4):1451–1456. doi: 10.1104/pp.84.4.1451. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Santoro C., Mermod N., Andrews P. C., Tjian R. A family of human CCAAT-box-binding proteins active in transcription and DNA replication: cloning and expression of multiple cDNAs. Nature. 1988 Jul 21;334(6179):218–224. doi: 10.1038/334218a0. [DOI] [PubMed] [Google Scholar]
  44. 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]
  45. Schindler U., Cashmore A. R. Photoregulated gene expression may involve ubiquitous DNA binding proteins. EMBO J. 1990 Nov;9(11):3415–3427. doi: 10.1002/j.1460-2075.1990.tb07549.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Schindler U., Menkens A. E., Beckmann H., Ecker J. R., Cashmore A. R. Heterodimerization between light-regulated and ubiquitously expressed Arabidopsis GBF bZIP proteins. EMBO J. 1992 Apr;11(4):1261–1273. doi: 10.1002/j.1460-2075.1992.tb05170.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Schulze-Lefert P., Dangl J. L., Becker-André M., Hahlbrock K., Schulz W. Inducible in vivo DNA footprints define sequences necessary for UV light activation of the parsley chalcone synthase gene. EMBO J. 1989 Mar;8(3):651–656. doi: 10.1002/j.1460-2075.1989.tb03422.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Singh K., Dennis E. S., Ellis J. G., Llewellyn D. J., Tokuhisa J. G., Wahleithner J. A., Peacock W. J. OCSBF-1, a maize ocs enhancer binding factor: isolation and expression during development. Plant Cell. 1990 Sep;2(9):891–903. doi: 10.1105/tpc.2.9.891. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Staiger D., Kaulen H., Schell J. A CACGTG motif of the Antirrhinum majus chalcone synthase promoter is recognized by an evolutionarily conserved nuclear protein. Proc Natl Acad Sci U S A. 1989 Sep;86(18):6930–6934. doi: 10.1073/pnas.86.18.6930. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Sun X. H., Baltimore D. An inhibitory domain of E12 transcription factor prevents DNA binding in E12 homodimers but not in E12 heterodimers. Cell. 1991 Jan 25;64(2):459–470. doi: 10.1016/0092-8674(91)90653-g. [DOI] [PubMed] [Google Scholar]
  51. Tabata T., Nakayama T., Mikami K., Iwabuchi M. HBP-1a and HBP-1b: leucine zipper-type transcription factors of wheat. EMBO J. 1991 Jun;10(6):1459–1467. doi: 10.1002/j.1460-2075.1991.tb07666.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. Tabata T., Takase H., Takayama S., Mikami K., Nakatsuka A., Kawata T., Nakayama T., Iwabuchi M. A protein that binds to a cis-acting element of wheat histone genes has a leucine zipper motif. Science. 1989 Sep 1;245(4921):965–967. doi: 10.1126/science.2772648. [DOI] [PubMed] [Google Scholar]
  53. Thiesen H. J., Bach C. Target Detection Assay (TDA): a versatile procedure to determine DNA binding sites as demonstrated on SP1 protein. Nucleic Acids Res. 1990 Jun 11;18(11):3203–3209. doi: 10.1093/nar/18.11.3203. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Webster N., Jin J. R., Green S., Hollis M., Chambon P. The yeast UASG is a transcriptional enhancer in human HeLa cells in the presence of the GAL4 trans-activator. Cell. 1988 Jan 29;52(2):169–178. doi: 10.1016/0092-8674(88)90505-3. [DOI] [PubMed] [Google Scholar]
  55. Weintraub H., Davis R., Tapscott S., Thayer M., Krause M., Benezra R., Blackwell T. K., Turner D., Rupp R., Hollenberg S. The myoD gene family: nodal point during specification of the muscle cell lineage. Science. 1991 Feb 15;251(4995):761–766. doi: 10.1126/science.1846704. [DOI] [PubMed] [Google Scholar]
  56. Weisshaar B., Armstrong G. A., Block A., da Costa e Silva O., Hahlbrock K. Light-inducible and constitutively expressed DNA-binding proteins recognizing a plant promoter element with functional relevance in light responsiveness. EMBO J. 1991 Jul;10(7):1777–1786. doi: 10.1002/j.1460-2075.1991.tb07702.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  57. Williams T., Admon A., Lüscher B., Tjian R. Cloning and expression of AP-2, a cell-type-specific transcription factor that activates inducible enhancer elements. Genes Dev. 1988 Dec;2(12A):1557–1569. doi: 10.1101/gad.2.12a.1557. [DOI] [PubMed] [Google Scholar]
  58. Williams T., Tjian R. Analysis of the DNA-binding and activation properties of the human transcription factor AP-2. Genes Dev. 1991 Apr;5(4):670–682. doi: 10.1101/gad.5.4.670. [DOI] [PubMed] [Google Scholar]
  59. Yamazaki K., Katagiri F., Imaseki H., Chua N. H. TGA1a, a tobacco DNA-binding protein, increases the rate of preinitiation complex formation in a plant in vitro transcription system [corrected]. Proc Natl Acad Sci U S A. 1990 Sep;87(18):7035–7039. doi: 10.1073/pnas.87.18.7035. [DOI] [PMC free article] [PubMed] [Google Scholar]
  60. Ziff E. B. Transcription factors: a new family gathers at the cAMP response site. Trends Genet. 1990 Mar;6(3):69–72. doi: 10.1016/0168-9525(90)90081-g. [DOI] [PubMed] [Google Scholar]

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