Abstract
Homeobox genes encode a large family of homeodomain proteins in animal systems. To test whether such genes are also abundant in higher plants, degenerate oligonucleotides complementary to sequences encoding the recognition helix (helix three) of the homeodomain were used to screen genomic and cDNA libraries from the plant Arabidopsis thaliana. Analysis of 8 of the 41 cDNAs isolated revealed that each encodes a presumptive homeodomain; interestingly, most of these clones also contain a leucine zipper motif tightly linked to the homeodomain. It is concluded that Arabidopsis encodes a large family of homeodomain proteins, including members that contain a homeodomain/leucine-zipper (HD-Zip) motif.
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- Agre P., Johnson P. F., McKnight S. L. Cognate DNA binding specificity retained after leucine zipper exchange between GCN4 and C/EBP. Science. 1989 Nov 17;246(4932):922–926. doi: 10.1126/science.2530632. [DOI] [PubMed] [Google Scholar]
- Bopp D., Burri M., Baumgartner S., Frigerio G., Noll M. Conservation of a large protein domain in the segmentation gene paired and in functionally related genes of Drosophila. Cell. 1986 Dec 26;47(6):1033–1040. doi: 10.1016/0092-8674(86)90818-4. [DOI] [PubMed] [Google Scholar]
- Braam J., Davis R. W. Rain-, wind-, and touch-induced expression of calmodulin and calmodulin-related genes in Arabidopsis. Cell. 1990 Feb 9;60(3):357–364. doi: 10.1016/0092-8674(90)90587-5. [DOI] [PubMed] [Google Scholar]
- Bürglin T. R., Finney M., Coulson A., Ruvkun G. Caenorhabditis elegans has scores of homoeobox-containing genes. Nature. 1989 Sep 21;341(6239):239–243. doi: 10.1038/341239a0. [DOI] [PubMed] [Google Scholar]
- Celniker S. E., Keelan D. J., Lewis E. B. The molecular genetics of the bithorax complex of Drosophila: characterization of the products of the Abdominal-B domain. Genes Dev. 1989 Sep;3(9):1424–1436. doi: 10.1101/gad.3.9.1424. [DOI] [PubMed] [Google Scholar]
- Chipperfield M., Maidek M., Pearson P., Ashburner M., Glover D. M., Saunders R. D., Duncan I., Hartl D., Merriam J., Lee G. Genome maps 1991 [wall chart]. Science. 1991 Oct 11;254(5029):247–262. doi: 10.1126/science.254.5029.247. [DOI] [PubMed] [Google Scholar]
- Elledge S. J., Mulligan J. T., Ramer S. W., Spottswood M., Davis R. W. Lambda YES: a multifunctional cDNA expression vector for the isolation of genes by complementation of yeast and Escherichia coli mutations. Proc Natl Acad Sci U S A. 1991 Mar 1;88(5):1731–1735. doi: 10.1073/pnas.88.5.1731. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 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]
- Gehring W. J., Müller M., Affolter M., Percival-Smith A., Billeter M., Qian Y. Q., Otting G., Wüthrich K. The structure of the homeodomain and its functional implications. Trends Genet. 1990 Oct;6(10):323–329. doi: 10.1016/0168-9525(90)90253-3. [DOI] [PubMed] [Google Scholar]
- Hanes S. D., Brent R. A genetic model for interaction of the homeodomain recognition helix with DNA. Science. 1991 Jan 25;251(4992):426–430. doi: 10.1126/science.1671176. [DOI] [PubMed] [Google Scholar]
- Hanes S. D., Brent R. DNA specificity of the bicoid activator protein is determined by homeodomain recognition helix residue 9. Cell. 1989 Jun 30;57(7):1275–1283. doi: 10.1016/0092-8674(89)90063-9. [DOI] [PubMed] [Google Scholar]
- Harrison S. C. A structural taxonomy of DNA-binding domains. Nature. 1991 Oct 24;353(6346):715–719. doi: 10.1038/353715a0. [DOI] [PubMed] [Google Scholar]
- Hayashi S., Scott M. P. What determines the specificity of action of Drosophila homeodomain proteins? Cell. 1990 Nov 30;63(5):883–894. doi: 10.1016/0092-8674(90)90492-w. [DOI] [PubMed] [Google Scholar]
- Hilson P., de Froidmont D., Lejour C., Hirai S., Jacquemin J. M., Yaniv M. Fos and Jun oncogenes transactivate chimeric or native promoters containing AP1/GCN4 binding sites in plant cells. Plant Cell. 1990 Jul;2(7):651–658. doi: 10.1105/tpc.2.7.651. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Jones N. Transcriptional regulation by dimerization: two sides to an incestuous relationship. Cell. 1990 Apr 6;61(1):9–11. doi: 10.1016/0092-8674(90)90207-u. [DOI] [PubMed] [Google Scholar]
- Kissinger C. R., Liu B. S., Martin-Blanco E., Kornberg T. B., Pabo C. O. Crystal structure of an engrailed homeodomain-DNA complex at 2.8 A resolution: a framework for understanding homeodomain-DNA interactions. Cell. 1990 Nov 2;63(3):579–590. doi: 10.1016/0092-8674(90)90453-l. [DOI] [PubMed] [Google Scholar]
- Kornfeld K., Saint R. B., Beachy P. A., Harte P. J., Peattie D. A., Hogness D. S. Structure and expression of a family of Ultrabithorax mRNAs generated by alternative splicing and polyadenylation in Drosophila. Genes Dev. 1989 Feb;3(2):243–258. doi: 10.1101/gad.3.2.243. [DOI] [PubMed] [Google Scholar]
- Landschulz W. H., Johnson P. F., Adashi E. Y., Graves B. J., McKnight S. L. Isolation of a recombinant copy of the gene encoding C/EBP. Genes Dev. 1988 Jul;2(7):786–800. doi: 10.1101/gad.2.7.786. [DOI] [PubMed] [Google Scholar]
- 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]
- 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]
- McGinnis W., Levine M. S., Hafen E., Kuroiwa A., Gehring W. J. A conserved DNA sequence in homoeotic genes of the Drosophila Antennapedia and bithorax complexes. 1984 Mar 29-Apr 4Nature. 308(5958):428–433. doi: 10.1038/308428a0. [DOI] [PubMed] [Google Scholar]
- O'Shea E. K., Klemm J. D., Kim P. S., Alber T. X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil. Science. 1991 Oct 25;254(5031):539–544. doi: 10.1126/science.1948029. [DOI] [PubMed] [Google Scholar]
- O'Shea E. K., Rutkowski R., Kim P. S. Evidence that the leucine zipper is a coiled coil. Science. 1989 Jan 27;243(4890):538–542. doi: 10.1126/science.2911757. [DOI] [PubMed] [Google Scholar]
- Ptashne M., Gann A. A. Activators and _targets. Nature. 1990 Jul 26;346(6282):329–331. doi: 10.1038/346329a0. [DOI] [PubMed] [Google Scholar]
- Rosner M. H., Vigano M. A., Ozato K., Timmons P. M., Poirier F., Rigby P. W., Staudt L. M. A POU-domain transcription factor in early stem cells and germ cells of the mammalian embryo. Nature. 1990 Jun 21;345(6277):686–692. doi: 10.1038/345686a0. [DOI] [PubMed] [Google Scholar]
- Ruberti I., Sessa G., Lucchetti S., Morelli G. A novel class of plant proteins containing a homeodomain with a closely linked leucine zipper motif. EMBO J. 1991 Jul;10(7):1787–1791. doi: 10.1002/j.1460-2075.1991.tb07703.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Schena M., Freedman L. P., Yamamoto K. R. Mutations in the glucocorticoid receptor zinc finger region that distinguish interdigitated DNA binding and transcriptional enhancement activities. Genes Dev. 1989 Oct;3(10):1590–1601. doi: 10.1101/gad.3.10.1590. [DOI] [PubMed] [Google Scholar]
- Schena M., Lloyd A. M., Davis R. W. A steroid-inducible gene expression system for plant cells. Proc Natl Acad Sci U S A. 1991 Dec 1;88(23):10421–10425. doi: 10.1073/pnas.88.23.10421. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Schena M. The evolutionary conservation of eukaryotic gene transcription. Experientia. 1989 Oct 15;45(10):972–983. doi: 10.1007/BF01953055. [DOI] [PubMed] [Google Scholar]
- Schena M., Yamamoto K. R. Mammalian glucocorticoid receptor derivatives enhance transcription in yeast. Science. 1988 Aug 19;241(4868):965–967. doi: 10.1126/science.3043665. [DOI] [PubMed] [Google Scholar]
- Scott M. P., Tamkun J. W., Hartzell G. W., 3rd The structure and function of the homeodomain. Biochim Biophys Acta. 1989 Jul 28;989(1):25–48. doi: 10.1016/0304-419x(89)90033-4. [DOI] [PubMed] [Google Scholar]
- Scott M. P., Weiner A. J. Structural relationships among genes that control development: sequence homology between the Antennapedia, Ultrabithorax, and fushi tarazu loci of Drosophila. Proc Natl Acad Sci U S A. 1984 Jul;81(13):4115–4119. doi: 10.1073/pnas.81.13.4115. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Sharrock R. A., Quail P. H. Novel phytochrome sequences in Arabidopsis thaliana: structure, evolution, and differential expression of a plant regulatory photoreceptor family. Genes Dev. 1989 Nov;3(11):1745–1757. doi: 10.1101/gad.3.11.1745. [DOI] [PubMed] [Google Scholar]
- Struhl K. Helix-turn-helix, zinc-finger, and leucine-zipper motifs for eukaryotic transcriptional regulatory proteins. Trends Biochem Sci. 1989 Apr;14(4):137–140. doi: 10.1016/0968-0004(89)90145-X. [DOI] [PubMed] [Google Scholar]
- Vollbrecht E., Veit B., Sinha N., Hake S. The developmental gene Knotted-1 is a member of a maize homeobox gene family. Nature. 1991 Mar 21;350(6315):241–243. doi: 10.1038/350241a0. [DOI] [PubMed] [Google Scholar]
- Walldorf U., Fleig R., Gehring W. J. Comparison of homeobox-containing genes of the honeybee and Drosophila. Proc Natl Acad Sci U S A. 1989 Dec;86(24):9971–9975. doi: 10.1073/pnas.86.24.9971. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wolberger C., Vershon A. K., Liu B., Johnson A. D., Pabo C. O. Crystal structure of a MAT alpha 2 homeodomain-operator complex suggests a general model for homeodomain-DNA interactions. Cell. 1991 Nov 1;67(3):517–528. doi: 10.1016/0092-8674(91)90526-5. [DOI] [PubMed] [Google Scholar]