Skip to main content
PMC home page
Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1996 Jul 9;93(14):6886–6891. doi: 10.1073/pnas.93.14.6886

Conservation and diversification in homeodomain-DNA interactions: a comparative genetic analysis.

D S Wilson 1, G Sheng 1, S Jun 1, C Desplan 1
PMCID: PMC38903  PMID: 8692913

Abstract

Nearly all metazoan homeodomains (HDs) possess DNA binding targets that are related by the presence of a TAAT sequence. We use an in vitro genetic DNA binding site selection assay to refine our understanding of the amino acid determinants for the recognition of the TAAT site. Superimposed upon the conserved ability of metazoan HDs to recognize a TAAT core is a difference in their preference for the bases that lie immediately 3' to it. Amino acid position 50 of the HD has been shown to discriminate among these base pairs, and structural studies have suggested that water-mediated hydrogen bonds and van der Waals contacts underlie for this ability. Here, we show that each of six amino acids tested at position 50 can confer a distinct DNA binding specificity.

Full text

PDF
6889

Images in this article

6890Fig. 4
on p.6890

Selected References

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

  1. Ades S. E., Sauer R. T. Differential DNA-binding specificity of the engrailed homeodomain: the role of residue 50. Biochemistry. 1994 Aug 9;33(31):9187–9194. doi: 10.1021/bi00197a022. [DOI] [PubMed] [Google Scholar]
  2. Andrés V., Chiara M. D., Mahdavi V. A new bipartite DNA-binding domain: cooperative interaction between the cut repeat and homeo domain of the cut homeo proteins. Genes Dev. 1994 Jan;8(2):245–257. doi: 10.1101/gad.8.2.245. [DOI] [PubMed] [Google Scholar]
  3. Beamer L. J., Pabo C. O. Refined 1.8 A crystal structure of the lambda repressor-operator complex. J Mol Biol. 1992 Sep 5;227(1):177–196. doi: 10.1016/0022-2836(92)90690-l. [DOI] [PubMed] [Google Scholar]
  4. Billeter M., Qian Y. Q., Otting G., Müller M., Gehring W., Wüthrich K. Determination of the nuclear magnetic resonance solution structure of an Antennapedia homeodomain-DNA complex. J Mol Biol. 1993 Dec 20;234(4):1084–1093. doi: 10.1006/jmbi.1993.1661. [DOI] [PubMed] [Google Scholar]
  5. Crompton M. R., Bartlett T. J., MacGregor A. D., Manfioletti G., Buratti E., Giancotti V., Goodwin G. H. Identification of a novel vertebrate homeobox gene expressed in haematopoietic cells. Nucleic Acids Res. 1992 Nov 11;20(21):5661–5667. doi: 10.1093/nar/20.21.5661. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Czerny T., Busslinger M. DNA-binding and transactivation properties of Pax-6: three amino acids in the paired domain are responsible for the different sequence recognition of Pax-6 and BSAP (Pax-5). Mol Cell Biol. 1995 May;15(5):2858–2871. doi: 10.1128/mcb.15.5.2858. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Ekker S. C., Jackson D. G., von Kessler D. P., Sun B. I., Young K. E., Beachy P. A. The degree of variation in DNA sequence recognition among four Drosophila homeotic proteins. EMBO J. 1994 Aug 1;13(15):3551–3560. doi: 10.1002/j.1460-2075.1994.tb06662.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. 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]
  9. 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]
  10. 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]
  11. Gehring W. J., Affolter M., Bürglin T. Homeodomain proteins. Annu Rev Biochem. 1994;63:487–526. doi: 10.1146/annurev.bi.63.070194.002415. [DOI] [PubMed] [Google Scholar]
  12. Gehring W. J., Qian Y. Q., Billeter M., Furukubo-Tokunaga K., Schier A. F., Resendez-Perez D., Affolter M., Otting G., Wüthrich K. Homeodomain-DNA recognition. Cell. 1994 Jul 29;78(2):211–223. doi: 10.1016/0092-8674(94)90292-5. [DOI] [PubMed] [Google Scholar]
  13. Gong Z., Hew C. L. Zinc and DNA binding properties of a novel LIM homeodomain protein Isl-2. Biochemistry. 1994 Dec 20;33(50):15149–15158. doi: 10.1021/bi00254a026. [DOI] [PubMed] [Google Scholar]
  14. 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]
  15. 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]
  16. Kalionis B., O'Farrell P. H. A universal target sequence is bound in vitro by diverse homeodomains. Mech Dev. 1993 Sep;43(1):57–70. doi: 10.1016/0925-4773(93)90023-q. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. 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]
  18. Klemm J. D., Rould M. A., Aurora R., Herr W., Pabo C. O. Crystal structure of the Oct-1 POU domain bound to an octamer site: DNA recognition with tethered DNA-binding modules. Cell. 1994 Apr 8;77(1):21–32. doi: 10.1016/0092-8674(94)90231-3. [DOI] [PubMed] [Google Scholar]
  19. Laughon A. DNA binding specificity of homeodomains. Biochemistry. 1991 Dec 3;30(48):11357–11367. doi: 10.1021/bi00112a001. [DOI] [PubMed] [Google Scholar]
  20. Li T., Stark M. R., Johnson A. D., Wolberger C. Crystal structure of the MATa1/MAT alpha 2 homeodomain heterodimer bound to DNA. Science. 1995 Oct 13;270(5234):262–269. doi: 10.1126/science.270.5234.262. [DOI] [PubMed] [Google Scholar]
  21. Nelson H. B., Laughon A. The DNA binding specificity of the Drosophila fushi tarazu protein: a possible role for DNA bending in homeodomain recognition. New Biol. 1990 Feb;2(2):171–178. [PubMed] [Google Scholar]
  22. 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]
  23. 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]
  24. Pick L., Schier A., Affolter M., Schmidt-Glenewinkel T., Gehring W. J. Analysis of the ftz upstream element: germ layer-specific enhancers are independently autoregulated. Genes Dev. 1990 Jul;4(7):1224–1239. doi: 10.1101/gad.4.7.1224. [DOI] [PubMed] [Google Scholar]
  25. Pomerantz J. L., Sharp P. A. Homeodomain determinants of major groove recognition. Biochemistry. 1994 Sep 13;33(36):10851–10858. doi: 10.1021/bi00202a001. [DOI] [PubMed] [Google Scholar]
  26. 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]
  27. Schier A. F., Gehring W. J. Direct homeodomain-DNA interaction in the autoregulation of the fushi tarazu gene. Nature. 1992 Apr 30;356(6372):804–807. doi: 10.1038/356804a0. [DOI] [PubMed] [Google Scholar]
  28. Sánchez-García I., Osada H., Forster A., Rabbitts T. H. The cysteine-rich LIM domains inhibit DNA binding by the associated homeodomain in Isl-1. EMBO J. 1993 Nov;12(11):4243–4250. doi: 10.1002/j.1460-2075.1993.tb06108.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. 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]
  30. 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]
  31. 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]
  32. 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]
  33. Wilson D. S., Guenther B., Desplan C., Kuriyan J. High resolution crystal structure of a paired (Pax) class cooperative homeodomain dimer on DNA. Cell. 1995 Sep 8;82(5):709–719. doi: 10.1016/0092-8674(95)90468-9. [DOI] [PubMed] [Google Scholar]
  34. Wilson D., Sheng G., Lecuit T., Dostatni N., Desplan C. Cooperative dimerization of paired class homeo domains on DNA. Genes Dev. 1993 Nov;7(11):2120–2134. doi: 10.1101/gad.7.11.2120. [DOI] [PubMed] [Google Scholar]
  35. 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]
  36. de Jong R., van der Heijden J., Meijlink F. DNA-binding specificity of the S8 homeodomain. Nucleic Acids Res. 1993 Oct 11;21(20):4711–4720. doi: 10.1093/nar/21.20.4711. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

RESOURCES