Skip to main content

Some NLM-NCBI services and products are experiencing heavy traffic, which may affect performance and availability. We apologize for the inconvenience and appreciate your patience. For assistance, please contact our Help Desk at info@ncbi.nlm.nih.gov.

Molecular and Cellular Biology logoLink to Molecular and Cellular Biology
. 1995 Aug;15(8):4076–4085. doi: 10.1128/mcb.15.8.4076

DNA binding specificity determinants in MADS-box transcription factors.

S J Nurrish 1, R Treisman 1
PMCID: PMC230646  PMID: 7623803

Abstract

The MADS box is a conserved sequence motif found in the DNA binding domain of a family of transcription factors which possess related but distinct DNA binding specificities. We investigated the basis of differential sequence recognition by the MADS-box proteins serum response factor (SRF), MCM1, and MEF2A, using chimeric proteins and site-directed mutants in conjunction with gel mobility shift and binding site selection assays. Deletion of sequences immediately N terminal to the SRF MADS box alters its preferred binding site to that of MEF2A, although the resulting protein still weakly binds SRF-specific sites: exclusive binding to MEF2 sites requires further mutations, at MADS-box residues 11 to 15. In contrast to SRF, the sequence specificity of MCM1 (and of MEF2A) is determined entirely by sequences within its MADS box, and mutation of only SRF MADS-box residue 1 is sufficient to alter its binding specificity to that of MCM1. However, changes at both MADS-box positions 1 and 11 to 15 are necessary and sufficient to alter the specificity of the MCM1 MADS box to that of MEF2, and vice versa. The role of SRF MADS-box residues which differ from those present in the other proteins was investigated by selection of functional SRF variants in yeast cells. SRF MADS-box position 1 was always a glycine in the variants, but many different sequences at the other nonconserved MADS-box residues were compatible with efficient DNA binding. We discuss potential mechanisms of DNA recognition by MADS-box proteins.

Full Text

The Full Text of this article is available as a PDF (643.1 KB).

Selected References

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

  1. Ammerer G. Identification, purification, and cloning of a polypeptide (PRTF/GRM) that binds to mating-specific promoter elements in yeast. Genes Dev. 1990 Feb;4(2):299–312. doi: 10.1101/gad.4.2.299. [DOI] [PubMed] [Google Scholar]
  2. Angel P., Baumann I., Stein B., Delius H., Rahmsdorf H. J., Herrlich P. 12-O-tetradecanoyl-phorbol-13-acetate induction of the human collagenase gene is mediated by an inducible enhancer element located in the 5'-flanking region. Mol Cell Biol. 1987 Jun;7(6):2256–2266. doi: 10.1128/mcb.7.6.2256. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Baumeister R., Helbl V., Hillen W. Contacts between Tet repressor and tet operator revealed by new recognition specificities of single amino acid replacement mutants. J Mol Biol. 1992 Aug 20;226(4):1257–1270. doi: 10.1016/0022-2836(92)91065-w. [DOI] [PubMed] [Google Scholar]
  4. Baumeister R., Müller G., Hecht B., Hillen W. Functional roles of amino acid residues involved in forming the alpha-helix-turn-alpha-helix operator DNA binding motif of Tet repressor from Tn10. Proteins. 1992 Oct;14(2):168–177. doi: 10.1002/prot.340140204. [DOI] [PubMed] [Google Scholar]
  5. Dalton S., Treisman R. Characterization of SAP-1, a protein recruited by serum response factor to the c-fos serum response element. Cell. 1992 Feb 7;68(3):597–612. doi: 10.1016/0092-8674(92)90194-h. [DOI] [PubMed] [Google Scholar]
  6. Hill C. S., Marais R., John S., Wynne J., Dalton S., Treisman R. Functional analysis of a growth factor-responsive transcription factor complex. Cell. 1993 Apr 23;73(2):395–406. doi: 10.1016/0092-8674(93)90238-l. [DOI] [PubMed] [Google Scholar]
  7. Huang H., Mizukami Y., Hu Y., Ma H. Isolation and characterization of the binding sequences for the product of the Arabidopsis floral homeotic gene AGAMOUS. Nucleic Acids Res. 1993 Oct 11;21(20):4769–4776. doi: 10.1093/nar/21.20.4769. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Huang L., Sera T., Schultz P. G. A permutational approach toward protein-DNA recognition. Proc Natl Acad Sci U S A. 1994 Apr 26;91(9):3969–3973. doi: 10.1073/pnas.91.9.3969. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Jarvis E. E., Clark K. L., Sprague G. F., Jr The yeast transcription activator PRTF, a homolog of the mammalian serum response factor, is encoded by the MCM1 gene. Genes Dev. 1989 Jul;3(7):936–945. doi: 10.1101/gad.3.7.936. [DOI] [PubMed] [Google Scholar]
  10. Marais R., Wynne J., Treisman R. The SRF accessory protein Elk-1 contains a growth factor-regulated transcriptional activation domain. Cell. 1993 Apr 23;73(2):381–393. doi: 10.1016/0092-8674(93)90237-k. [DOI] [PubMed] [Google Scholar]
  11. Messenguy F., Dubois E. Genetic evidence for a role for MCM1 in the regulation of arginine metabolism in Saccharomyces cerevisiae. Mol Cell Biol. 1993 Apr;13(4):2586–2592. doi: 10.1128/mcb.13.4.2586. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Mueller C. G., Nordheim A. A protein domain conserved between yeast MCM1 and human SRF directs ternary complex formation. EMBO J. 1991 Dec;10(13):4219–4229. doi: 10.1002/j.1460-2075.1991.tb05000.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Norman C., Runswick M., Pollock R., Treisman R. Isolation and properties of cDNA clones encoding SRF, a transcription factor that binds to the c-fos serum response element. Cell. 1988 Dec 23;55(6):989–1003. doi: 10.1016/0092-8674(88)90244-9. [DOI] [PubMed] [Google Scholar]
  14. Passmore S., Maine G. T., Elble R., Christ C., Tye B. K. Saccharomyces cerevisiae protein involved in plasmid maintenance is necessary for mating of MAT alpha cells. J Mol Biol. 1988 Dec 5;204(3):593–606. doi: 10.1016/0022-2836(88)90358-0. [DOI] [PubMed] [Google Scholar]
  15. 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]
  16. Pollock R., Treisman R. Human SRF-related proteins: DNA-binding properties and potential regulatory targets. Genes Dev. 1991 Dec;5(12A):2327–2341. doi: 10.1101/gad.5.12a.2327. [DOI] [PubMed] [Google Scholar]
  17. Pu W. T., Struhl K. Highly conserved residues in the bZIP domain of yeast GCN4 are not essential for DNA binding. Mol Cell Biol. 1991 Oct;11(10):4918–4926. doi: 10.1128/mcb.11.10.4918. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Rost B., Sander C. Prediction of protein secondary structure at better than 70% accuracy. J Mol Biol. 1993 Jul 20;232(2):584–599. doi: 10.1006/jmbi.1993.1413. [DOI] [PubMed] [Google Scholar]
  19. Schwarz-Sommer Z., Huijser P., Nacken W., Saedler H., Sommer H. Genetic Control of Flower Development by Homeotic Genes in Antirrhinum majus. Science. 1990 Nov 16;250(4983):931–936. doi: 10.1126/science.250.4983.931. [DOI] [PubMed] [Google Scholar]
  20. Sharrocks A. D., Gille H., Shaw P. E. Identification of amino acids essential for DNA binding and dimerization in p67SRF: implications for a novel DNA-binding motif. Mol Cell Biol. 1993 Jan;13(1):123–132. doi: 10.1128/mcb.13.1.123. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Sharrocks A. D., von Hesler F., Shaw P. E. The identification of elements determining the different DNA binding specificities of the MADS box proteins p67SRF and RSRFC4. Nucleic Acids Res. 1993 Jan 25;21(2):215–221. doi: 10.1093/nar/21.2.215. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Sommer H., Beltrán J. P., Huijser P., Pape H., Lönnig W. E., Saedler H., Schwarz-Sommer Z. Deficiens, a homeotic gene involved in the control of flower morphogenesis in Antirrhinum majus: the protein shows homology to transcription factors. EMBO J. 1990 Mar;9(3):605–613. doi: 10.1002/j.1460-2075.1990.tb08152.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Suzuki M. Common features in DNA recognition helices of eukaryotic transcription factors. EMBO J. 1993 Aug;12(8):3221–3226. doi: 10.1002/j.1460-2075.1993.tb05991.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Treisman R., Ammerer G. The SRF and MCM1 transcription factors. Curr Opin Genet Dev. 1992 Apr;2(2):221–226. doi: 10.1016/s0959-437x(05)80277-1. [DOI] [PubMed] [Google Scholar]
  25. Treisman R. Identification and purification of a polypeptide that binds to the c-fos serum response element. EMBO J. 1987 Sep;6(9):2711–2717. doi: 10.1002/j.1460-2075.1987.tb02564.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Wynne J., Treisman R. SRF and MCM1 have related but distinct DNA binding specificities. Nucleic Acids Res. 1992 Jul 11;20(13):3297–3303. doi: 10.1093/nar/20.13.3297. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Yanofsky M. F., Ma H., Bowman J. L., Drews G. N., Feldmann K. A., Meyerowitz E. M. The protein encoded by the Arabidopsis homeotic gene agamous resembles transcription factors. Nature. 1990 Jul 5;346(6279):35–39. doi: 10.1038/346035a0. [DOI] [PubMed] [Google Scholar]
  28. Yu Y. T., Breitbart R. E., Smoot L. B., Lee Y., Mahdavi V., Nadal-Ginard B. Human myocyte-specific enhancer factor 2 comprises a group of tissue-restricted MADS box transcription factors. Genes Dev. 1992 Sep;6(9):1783–1798. doi: 10.1101/gad.6.9.1783. [DOI] [PubMed] [Google Scholar]

Articles from Molecular and Cellular Biology are provided here courtesy of Taylor & Francis

RESOURCES