Skip to main content
Log in

DNA-binding and dimerization preferences of Arabidopsis homeodomain-leucine zipper transcription factors in vitro

  • Published:
Plant Molecular Biology Aims and scope Submit manuscript

Abstract

Homeodomain-leucine zipper (HDZip) proteins constitute a large family of transcription factors apparently unique to plants. In this report we characterize the DNA-binding and dimerization preferences in vitro of class I HDZip proteins. Using gel-exclusion chromatography and in vitro protein binding assays we demonstrate that the HDZip class I protein ATHB5 forms a homodimeric complex in solution. Consistent with this finding we have demonstrated the sequence-specific interaction of ATHB5 with a 9 bp pseudopalindromic DNA sequence, CAATNATTG, composed of two half-sites overlapping at a central position, by use of a PCR-assisted binding-site selection assay and competitive EMSA experiments. A majority of other known members of HDZip class I interacted with similar DNA sequences, but differed in their preference for A/T versus G/C in the central position of the binding site. Selective heterodimerization in vitro was demonstrated between ATHB5 and different class I HDZip proteins. Heterodimer formation between class I HDZip proteins is of potential functional significance for the integration of information from different signalling pathways in the control of plant development.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Aoyama, T., Dong, C.H., Wu, Y., Carabelli, M., Sessa, G., Ruberti, I., Morelli, G. and Chua, N.H. 1995. Ectopic expression of the Arabidopsis transcriptional activator Athb-1 alters leaf cell fate in tobacco. Plant Cell 7: 1773–1785.

    Google Scholar 

  • Baima, S., Nobili, F., Sessa, G., Lucchetti, S., Ruberti, I. and Morelli, G. 1995. The expression of the Athb-8 homeobox gene is restricted to provascular cells in Arabidopsis thaliana. Development 121: 4171–4182.

    Google Scholar 

  • Carabelli, M., Sessa, G., Baima, S., Morelli, G. and Ruberti, I. 1993. The Arabidopsis Athb-2 and -4 genes are strongly induced by far-red-rich light. Plant J. 4: 469–479.

    Google Scholar 

  • Carabelli, M., Morelli, G., Whitelam, G. and Ruberti, I. 1996. Twilight-zone and canopy shade induction of the Athb-2 home-obox gene in green plants. Proc. Natl. Acad. Sci. USA 93: 3530–3535.

    Google Scholar 

  • Di Cristina, M., Sessa, G., Dolan, L., Linstead, P., Baima, S., Ruberti, I. and Morelli, G. 1996. The Arabidopsis Athb-10 (GLABRA2) is an HD-Zip protein required for regulation of root hair development. Plant J. 10: 393–402.

    Google Scholar 

  • Ellenberger, T.E., Brandl, C.J., Struhl, K. and Harrison, S.C. 1992. The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted alpha helices: crystal structure of the protein-DNA complex. Cell 24: 1223–1237.

    Google Scholar 

  • Ekker, S.C., Young, K.E., von Kessler, D.P. and Beachy, P.A. 1991. Optimal DNA sequence recognition by the Ultrabithorax homeodomain of Drosophila. EMBO J. 10: 1179–1186.

    Google Scholar 

  • Frank, W., Phillips, J., Salamini, F. and Bartels, D. 1998. Two dehydration-inducible transcripts from the resurrection plant Craterostigma plantagineum encode interacting homeodomain-leucine zipper proteins. Plant J. 15: 413–421.

    Google Scholar 

  • Glover, J.N. and Harrison, S.C. 1995. Crystal structure of the het-erodimeric bZIP transcription factor c-Fos-c-Jun bound to DNA. Nature 373: 257–261.

    Google Scholar 

  • Lee, Y.H. and Chun, J.Y. 1998. A new homeodomain-leucine zip-per gene from Arabidopsis thaliana induced by water stress and abscisic acid treatment. Plant Mol. Biol. 37: 377–384.

    Google Scholar 

  • Lemercier, C., To, R.Q., Carrasco, R.A. and Konieczny S.F. 1998. The basic helix-loop-helix transcription factor Mist1 functions as a transcriptional repressor of MyoD. EMBO J. 17: 1412–1422.

    Google Scholar 

  • Mattsson, J., Söderman, E., Svenson, M., Borkird, C., and Engström, P. 1992. A new homeobox-leucine zipper gene from Arabidopsis thaliana. Plant Mol. Biol. 18: 1019–1022.

    Google Scholar 

  • Meijer, A.H., Scarpella, E., van Dijk, E.L., Qin, L., Taal, A.J., Rueb, S., Harrington, S.E., McCouch, S.R., Schilperoort, R.A. and Hoge, J.H. 1997. Transcriptional repression by Oshox1, a novel homeodomain leucine zipper protein from rice. Plant J. 11: 263–276.

    Google Scholar 

  • Menkens, A.E. and Cashmore, A.R. 1994. Isolation and character-ization of a fourth Arabidopsis thaliana G-box-binding factor, which has similarities to Fos oncoprotein. Proc. Natl. Acad. Sci. USA 91: 2522–2526.

    Google Scholar 

  • Oliphant, A.R., Brandl, C.J. and Struhl, K. 1989. Defining the se-quence specificity of DNA-binding proteins by selecting binding sites from random-sequence oligonucleotides: analysis of yeast GCN4 protein. Mol. Cell. Biol. 9: 2944–2949.

    Google Scholar 

  • O'shea, E.K., Rutkowski, R. and Kim, P.S. 1992. Mechanism of specificity in the Fos-Jun oncoprotein heterodimer. Cell 68: 699–708.

    Google Scholar 

  • Pollock, R. and Treisman, R.A. 1990. A sensitive method for the determination of protein-DNA binding specificities. Nucl. Acids Res. 18: 6197–6204.

    Google Scholar 

  • Rerie, W.G., Feldmann, K.A. and Marks, M.D. 1994. The GLABRA2 gene encodes a homeo domain protein required for normal trichome development in Arabidopsis. Genes Dev. 8: 1388–1399.

    Google Scholar 

  • Ruberti, I., Sessa, G., Lucchetti, S. and Morelli, G. 1991. A novel class of plant proteins containing a homeodomain with a closely linked leucine zipper motif. EMBO J. 10: 1787–1791.

    Google Scholar 

  • Sambrook, J., Fritsch, E.F. and Maniatis, T. 1989. Molecular Cloning: A Laboratory Manual, 2nd ed. Cold Spring Harbor Laboratory Press, Plainview, NY.

    Google Scholar 

  • Schindler, U., Terzaghi, W., Beckmann, H., Kadesch, T., and Cashmore, A.R. 1992. DNA binding site preferences and tran-scriptional activation properties of the Arabidopsis transcription factor GBF1. EMBO J. 11: 1275–1289.

    Google Scholar 

  • Schena, M. and Davis, R.W. 1992. HD-Zip proteins: members of an Arabidopsis homeodomain protein superfamily. Proc. Natl. Acad. Sci. USA 89: 3894–3898.

    Google Scholar 

  • Schena, M. and Davis, R.W. 1994. Structure of homeobox-leucine zipper genes suggests a model for the evolution of gene families. Proc. Natl. Acad. Sci. USA 91: 8393–8397.

    Google Scholar 

  • Schuermann, M., Hunter, J.B., Hennig, G. and Muller, R. 1991. Non-leucine residues in the leucine repeats of Fos and Jun contribute to the stability and determine the specificity of dimer-ization. Nucl. Acids Res. 19: 739–746.

    Google Scholar 

  • Sessa, G., Morelli, G. and Ruberti, I. 1993. The Athb-1 and-2 HD-Zip domains homodimerize forming complexes of different DNA binding specificities. EMBO J. 12: 3507–3517.

    Google Scholar 

  • Sessa, G., Carabelli, M., Ruberti, I., Lucchetti, S., Baima, S. and Morelli, G. 1994. Identification of distinct families of HD-Zip proteins in Arabidopsis thaliana. In: P. Puigdomènech and G. Coruzzi (Eds.) Molecular-Genetic Analysis of Plant Develop-ment and Metabolism, Springer-Verlag, Berlin, pp. 411–426.

    Google Scholar 

  • Sessa, G., Morelli, G. and Ruberti, I. 1997. DNA-binding specificity of the homeodomain-leucine zipper domain. J. Mol. Biol. 274: 303–309.

    Google Scholar 

  • Sessa, G., Steindler, C., Morelli, G. and Ruberti, I. 1998. The Ara-bidopsis Athb-8, -9 and -14 genes are members of a small gene family coding for highly related HD-ZIP proteins. Plant Mol. Biol. 38: 609–622.

    Google Scholar 

  • Steindler, C., Matteucci, A., Sessa, G., Weimar, T., Ohgishi, M., Aoyama, T., Morelli, G. and Ruberti, I. 1999. Shade avoidance responses are mediated by the ATHB-2 HD-Zip pro-tein, a negative regulator of gene expression. Development 126: 4235–4245.

    Google Scholar 

  • Söderman, E. 1996. Genes encoding homeodomain-leucine zipper proteins in Arabidopsis thaliana. Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 247, Uppsala, Acta Universitas Upsaliensis.

    Google Scholar 

  • Söderman, E., Mattsson, J., Svenson, M., Borkird, C. and Engström, P. 1994. Expression patterns of novel genes encoding home-odomain leucine-zipper proteins in Arabidopsis thaliana. Plant Mol. Biol. 26: 145–154.

    Google Scholar 

  • Söderman, E., Mattsson, J. and Engström, P. 1996. The Arabidop-sis homeobox gene ATHB-7 is induced by water deficit and by abscisic acid. Plant J. 10: 375–381.

    Google Scholar 

  • Verrijzer, C.P., Alkema, M.J., van Weperen, W.W., van Leeuwen, H.C., Strating, M.J. and van der Vliet, P.C. 1992. The DNA binding specificity of the bipartite POU domain and its subdomains. EMBO J. 11: 4993–5003.

    Google Scholar 

  • Vinson, C.R., Hai, T. and Boyd, S.M. 1993. Dimerization specificity of the leucine zipper-containing bZIP motif on DNA binding: prediction and rational design. Genes Dev. 7: 1047–1058.

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Rights and permissions

Reprints and permissions

About this article

Cite this article

Johannesson, H., Wang, Y. & Engström, P. DNA-binding and dimerization preferences of Arabidopsis homeodomain-leucine zipper transcription factors in vitro. Plant Mol Biol 45, 63–73 (2001). https://doi.org/10.1023/A:1006423324025

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1023/A:1006423324025

Navigation