Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1993 Oct 11;21(20):4711–4720. doi: 10.1093/nar/21.20.4711

DNA-binding specificity of the S8 homeodomain.

R de Jong 1, J van der Heijden 1, F Meijlink 1
PMCID: PMC331495  PMID: 7901837

Abstract

The murine S8 homeobox gene is expressed in a mesenchyme-specific pattern in embryos, as well as in mesodermal cell lines. The S8 homeodomain is overall similar to paired type homeodomains, but at position 50, which is crucial for specific DNA recognition, it contains a Gln, as is found in Antennapedia (Antp)-type homeodomains. We determined the DNA-binding specificity of the purified S8 homeodomain by in vitro selection of random oligonucleotides. The resulting 11-bp consensus binding site, ANC/TC/TAATTAA/GC resembles, but subtly differs from, the recognition sequences of Antp-type homeodomains. Equilibrium binding constants of down to 6.0 x 10(-10) M were found for binding of the S8 homeodomain to selected oligonucleotides. Using specific antibodies and an oligonucleotide containing an S8-site, we detected by band-shift two abundant DNA binding activities in mesodermal cell lines that correspond to S8 and two more that correspond to its close relative MHox. These S8 protein forms are differentially expressed in retinoic acid-treated P19 EC cells.

Full text

PDF
4713

Images in this article

4713Image
on p.4713
4714Image
on p.4714
4716Image
on p.4716
4716Image
on p.4716

Selected References

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

  1. Affolter M., Percival-Smith A., Müller M., Leupin W., Gehring W. J. DNA binding properties of the purified Antennapedia homeodomain. Proc Natl Acad Sci U S A. 1990 Jun;87(11):4093–4097. doi: 10.1073/pnas.87.11.4093. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Baumgartner S., Bopp D., Burri M., Noll M. Structure of two genes at the gooseberry locus related to the paired gene and their spatial expression during Drosophila embryogenesis. Genes Dev. 1987 Dec;1(10):1247–1267. doi: 10.1101/gad.1.10.1247. [DOI] [PubMed] [Google Scholar]
  3. Berk A. J. Regulation of eukaryotic transcription factors by post-translational modification. Biochim Biophys Acta. 1989 Nov 2;1009(2):103–109. doi: 10.1016/0167-4781(89)90087-0. [DOI] [PubMed] [Google Scholar]
  4. 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]
  5. 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]
  6. Catron K. M., Iler N., Abate C. Nucleotides flanking a conserved TAAT core dictate the DNA binding specificity of three murine homeodomain proteins. Mol Cell Biol. 1993 Apr;13(4):2354–2365. doi: 10.1128/mcb.13.4.2354. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Chalepakis G., Fritsch R., Fickenscher H., Deutsch U., Goulding M., Gruss P. The molecular basis of the undulated/Pax-1 mutation. Cell. 1991 Sep 6;66(5):873–884. doi: 10.1016/0092-8674(91)90434-z. [DOI] [PubMed] [Google Scholar]
  8. Corsetti M. T., Briata P., Sanseverino L., Daga A., Airoldi I., Simeone A., Palmisano G., Angelini C., Boncinelli E., Corte G. Differential DNA binding properties of three human homeodomain proteins. Nucleic Acids Res. 1992 Sep 11;20(17):4465–4472. doi: 10.1093/nar/20.17.4465. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Cserjesi P., Lilly B., Bryson L., Wang Y., Sassoon D. A., Olson E. N. MHox: a mesodermally restricted homeodomain protein that binds an essential site in the muscle creatine kinase enhancer. Development. 1992 Aug;115(4):1087–1101. doi: 10.1242/dev.115.4.1087. [DOI] [PubMed] [Google Scholar]
  10. Damante G., Di Lauro R. Several regions of Antennapedia and thyroid transcription factor 1 homeodomains contribute to DNA binding specificity. Proc Natl Acad Sci U S A. 1991 Jun 15;88(12):5388–5392. doi: 10.1073/pnas.88.12.5388. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Dear T. N., Sanchez-Garcia I., Rabbitts T. H. The HOX11 gene encodes a DNA-binding nuclear transcription factor belonging to a distinct family of homeobox genes. Proc Natl Acad Sci U S A. 1993 May 15;90(10):4431–4435. doi: 10.1073/pnas.90.10.4431. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Dessain S., Gross C. T., Kuziora M. A., McGinnis W. Antp-type homeodomains have distinct DNA binding specificities that correlate with their different regulatory functions in embryos. EMBO J. 1992 Mar;11(3):991–1002. doi: 10.1002/j.1460-2075.1992.tb05138.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. 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]
  14. Ekker S. C., von Kessler D. P., Beachy P. A. Differential DNA sequence recognition is a determinant of specificity in homeotic gene action. EMBO J. 1992 Nov;11(11):4059–4072. doi: 10.1002/j.1460-2075.1992.tb05499.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Florence B., Handrow R., Laughon A. DNA-binding specificity of the fushi tarazu homeodomain. Mol Cell Biol. 1991 Jul;11(7):3613–3623. doi: 10.1128/mcb.11.7.3613. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Grueneberg D. A., Natesan S., Alexandre C., Gilman M. Z. Human and Drosophila homeodomain proteins that enhance the DNA-binding activity of serum response factor. Science. 1992 Aug 21;257(5073):1089–1095. doi: 10.1126/science.257.5073.1089. [DOI] [PubMed] [Google Scholar]
  17. Gruss P., Walther C. Pax in development. Cell. 1992 May 29;69(5):719–722. doi: 10.1016/0092-8674(92)90281-g. [DOI] [PubMed] [Google Scholar]
  18. 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]
  19. 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]
  20. Hawkins N. C., McGhee J. D. Homeobox containing genes in the nematode Caenorhabditis elegans. Nucleic Acids Res. 1990 Oct 25;18(20):6101–6106. doi: 10.1093/nar/18.20.6101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. 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]
  22. Hoey T., Warrior R., Manak J., Levine M. DNA-binding activities of the Drosophila melanogaster even-skipped protein are mediated by its homeo domain and influenced by protein context. Mol Cell Biol. 1988 Nov;8(11):4598–4607. doi: 10.1128/mcb.8.11.4598. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Jones-Villeneuve E. M., McBurney M. W., Rogers K. A., Kalnins V. I. Retinoic acid induces embryonal carcinoma cells to differentiate into neurons and glial cells. J Cell Biol. 1982 Aug;94(2):253–262. doi: 10.1083/jcb.94.2.253. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Kern M. J., Witte D. P., Valerius M. T., Aronow B. J., Potter S. S. A novel murine homeobox gene isolated by a tissue specific PCR cloning strategy. Nucleic Acids Res. 1992 Oct 11;20(19):5189–5195. doi: 10.1093/nar/20.19.5189. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Kessel M., Gruss P. Murine developmental control genes. Science. 1990 Jul 27;249(4967):374–379. doi: 10.1126/science.1974085. [DOI] [PubMed] [Google Scholar]
  26. 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]
  27. Kongsuwan K., Webb E., Housiaux P., Adams J. M. Expression of multiple homeobox genes within diverse mammalian haemopoietic lineages. EMBO J. 1988 Jul;7(7):2131–2138. doi: 10.1002/j.1460-2075.1988.tb03052.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Kuziora M. A., McGinnis W. A homeodomain substitution changes the regulatory specificity of the deformed protein in Drosophila embryos. Cell. 1989 Nov 3;59(3):563–571. doi: 10.1016/0092-8674(89)90039-1. [DOI] [PubMed] [Google Scholar]
  29. Laughon A. DNA binding specificity of homeodomains. Biochemistry. 1991 Dec 3;30(48):11357–11367. doi: 10.1021/bi00112a001. [DOI] [PubMed] [Google Scholar]
  30. 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]
  31. Lee K. A., Bindereif A., Green M. R. A small-scale procedure for preparation of nuclear extracts that support efficient transcription and pre-mRNA splicing. Gene Anal Tech. 1988 Mar-Apr;5(2):22–31. doi: 10.1016/0735-0651(88)90023-4. [DOI] [PubMed] [Google Scholar]
  32. Lin L., McGinnis W. Mapping functional specificity in the Dfd and Ubx homeo domains. Genes Dev. 1992 Jun;6(6):1071–1081. doi: 10.1101/gad.6.6.1071. [DOI] [PubMed] [Google Scholar]
  33. 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]
  34. Odenwald W. F., Garbern J., Arnheiter H., Tournier-Lasserve E., Lazzarini R. A. The Hox-1.3 homeo box protein is a sequence-specific DNA-binding phosphoprotein. Genes Dev. 1989 Feb;3(2):158–172. doi: 10.1101/gad.3.2.158. [DOI] [PubMed] [Google Scholar]
  35. Oliphant A. R., Brandl C. J., Struhl K. Defining the sequence specificity of DNA-binding proteins by selecting binding sites from random-sequence oligonucleotides: analysis of yeast GCN4 protein. Mol Cell Biol. 1989 Jul;9(7):2944–2949. doi: 10.1128/mcb.9.7.2944. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Opstelten D. J., Vogels R., Robert B., Kalkhoven E., Zwartkruis F., de Laaf L., Destrée O. H., Deschamps J., Lawson K. A., Meijlink F. The mouse homeobox gene, S8, is expressed during embryogenesis predominantly in mesenchyme. Mech Dev. 1991 Mar;34(1):29–41. doi: 10.1016/0925-4773(91)90089-o. [DOI] [PubMed] [Google Scholar]
  37. Otting G., Qian Y. Q., Billeter M., Müller M., Affolter M., Gehring W. J., Wüthrich K. Protein--DNA contacts in the structure of a homeodomain--DNA complex determined by nuclear magnetic resonance spectroscopy in solution. EMBO J. 1990 Oct;9(10):3085–3092. doi: 10.1002/j.1460-2075.1990.tb07505.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Percival-Smith A., Müller M., Affolter M., Gehring W. J. The interaction with DNA of wild-type and mutant fushi tarazu homeodomains. EMBO J. 1990 Dec;9(12):3967–3974. doi: 10.1002/j.1460-2075.1990.tb07617.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Pollock R., Treisman R. A sensitive method for the determination of protein-DNA binding specificities. Nucleic Acids Res. 1990 Nov 11;18(21):6197–6204. doi: 10.1093/nar/18.21.6197. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Qian Y. Q., Billeter M., Otting G., Müller M., Gehring W. J., Wüthrich K. The structure of the Antennapedia homeodomain determined by NMR spectroscopy in solution: comparison with prokaryotic repressors. Cell. 1989 Nov 3;59(3):573–580. doi: 10.1016/0092-8674(89)90040-8. [DOI] [PubMed] [Google Scholar]
  41. Rosa F. M. Mix.1, a homeobox mRNA inducible by mesoderm inducers, is expressed mostly in the presumptive endodermal cells of Xenopus embryos. Cell. 1989 Jun 16;57(6):965–974. doi: 10.1016/0092-8674(89)90335-8. [DOI] [PubMed] [Google Scholar]
  42. Schneitz K., Spielmann P., Noll M. Molecular genetics of aristaless, a prd-type homeo box gene involved in the morphogenesis of proximal and distal pattern elements in a subset of appendages in Drosophila. Genes Dev. 1993 Jan;7(1):114–129. doi: 10.1101/gad.7.1.114. [DOI] [PubMed] [Google Scholar]
  43. 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]
  44. Studier F. W., Rosenberg A. H., Dunn J. J., Dubendorff J. W. Use of T7 RNA polymerase to direct expression of cloned genes. Methods Enzymol. 1990;185:60–89. doi: 10.1016/0076-6879(90)85008-c. [DOI] [PubMed] [Google Scholar]
  45. Treisman J., Gönczy P., Vashishtha M., Harris E., Desplan C. A single amino acid can determine the DNA binding specificity of homeodomain proteins. Cell. 1989 Nov 3;59(3):553–562. doi: 10.1016/0092-8674(89)90038-x. [DOI] [PubMed] [Google Scholar]
  46. Treisman J., Harris E., Desplan C. The paired box encodes a second DNA-binding domain in the paired homeo domain protein. Genes Dev. 1991 Apr;5(4):594–604. doi: 10.1101/gad.5.4.594. [DOI] [PubMed] [Google Scholar]
  47. Treisman J., Harris E., Wilson D., Desplan C. The homeodomain: a new face for the helix-turn-helix? Bioessays. 1992 Mar;14(3):145–150. doi: 10.1002/bies.950140302. [DOI] [PubMed] [Google Scholar]
  48. Verrijzer C. P., Alkema M. J., van Weperen W. W., Van Leeuwen H. C., Strating M. J., van der Vliet P. C. The DNA binding specificity of the bipartite POU domain and its subdomains. EMBO J. 1992 Dec;11(13):4993–5003. doi: 10.1002/j.1460-2075.1992.tb05606.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Webster P. J., Mansour T. E. Conserved classes of homeodomains in Schistosoma mansoni, an early bilateral metazoan. Mech Dev. 1992 Jul;38(1):25–32. doi: 10.1016/0925-4773(92)90035-i. [DOI] [PubMed] [Google Scholar]
  50. 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]
  51. de Jong R., Meijlink F. The homeobox gene S8: mesoderm-specific expression in presomite embryos and in cells cultured in vitro and modulation in differentiating pluripotent cells. Dev Biol. 1993 May;157(1):133–146. doi: 10.1006/dbio.1993.1118. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES