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. 1997 May;17(5):2876–2887. doi: 10.1128/mcb.17.5.2876

DNA binding by MADS-box transcription factors: a molecular mechanism for differential DNA bending.

A G West 1, P Shore 1, A D Sharrocks 1
PMCID: PMC232140  PMID: 9111360

Abstract

The serum response factor (SRF) and myocyte enhancer factor 2A (MEF2A) represent two human members of the MADS-box transcription factor family. Each protein has a distinct biological function which is reflected by the distinct specificities of the proteins for coregulatory protein partners and DNA-binding sites. In this study, we have investigated the mechanism of DNA binding utilized by these two related transcription factors. Although SRF and MEF2A belong to the same family and contain related DNA-binding domains, their DNA-binding mechanisms differ in several key aspects. In contrast to the dramatic DNA bending induced by SRF, MEF2A induces minimal DNA distortion. A combination of loss- and gain-of-function mutagenesis identified a single amino acid residue located at the N terminus of the recognition helices as the critical mediator of this differential DNA bending. This residue is also involved in determining DNA-binding specificity, thus indicating a link between DNA bending and DNA-binding specificity determination. Furthermore, different basic residues within the putative recognition alpha-helices are critical for DNA binding, and the role of the C-terminal extensions to the MADS box in dimerization between SRF and MEF2A also differs. These important differences in the molecular interactions of SRF and MEF2A are likely to contribute to their differing roles in the regulation of specific gene transcription.

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Selected References

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  1. Breitbart R. E., Liang C. S., Smoot L. B., Laheru D. A., Mahdavi V., Nadal-Ginard B. A fourth human MEF2 transcription factor, hMEF2D, is an early marker of the myogenic lineage. Development. 1993 Aug;118(4):1095–1106. doi: 10.1242/dev.118.4.1095. [DOI] [PubMed] [Google Scholar]
  2. Buckingham M. Molecular biology of muscle development. Cell. 1994 Jul 15;78(1):15–21. doi: 10.1016/0092-8674(94)90568-1. [DOI] [PubMed] [Google Scholar]
  3. Cowell I. G., Skinner A., Hurst H. C. Transcriptional repression by a novel member of the bZIP family of transcription factors. Mol Cell Biol. 1992 Jul;12(7):3070–3077. doi: 10.1128/mcb.12.7.3070. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Cress W. D., Nevins J. R. A role for a bent DNA structure in E2F-mediated transcription activation. Mol Cell Biol. 1996 May;16(5):2119–2127. doi: 10.1128/mcb.16.5.2119. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Derbyshire K. M., Salvo J. J., Grindley N. D. A simple and efficient procedure for saturation mutagenesis using mixed oligodeoxynucleotides. Gene. 1986;46(2-3):145–152. doi: 10.1016/0378-1119(86)90398-7. [DOI] [PubMed] [Google Scholar]
  6. Dolan J. W., Fields S. Cell-type-specific transcription in yeast. Biochim Biophys Acta. 1991 Feb 16;1088(2):155–169. doi: 10.1016/0167-4781(91)90051-m. [DOI] [PubMed] [Google Scholar]
  7. Drak J., Crothers D. M. Helical repeat and chirality effects on DNA gel electrophoretic mobility. Proc Natl Acad Sci U S A. 1991 Apr 15;88(8):3074–3078. doi: 10.1073/pnas.88.8.3074. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Gustafson T. A., Taylor A., Kedes L. DNA bending is induced by a transcription factor that interacts with the human c-FOS and alpha-actin promoters. Proc Natl Acad Sci U S A. 1989 Apr;86(7):2162–2166. doi: 10.1073/pnas.86.7.2162. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Kahn J. D., Crothers D. M. Protein-induced bending and DNA cyclization. Proc Natl Acad Sci U S A. 1992 Jul 15;89(14):6343–6347. doi: 10.1073/pnas.89.14.6343. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Kaushal S., Schneider J. W., Nadal-Ginard B., Mahdavi V. Activation of the myogenic lineage by MEF2A, a factor that induces and cooperates with MyoD. Science. 1994 Nov 18;266(5188):1236–1240. doi: 10.1126/science.7973707. [DOI] [PubMed] [Google Scholar]
  11. Kerppola T. K., Curran T. Selective DNA bending by a variety of bZIP proteins. Mol Cell Biol. 1993 Sep;13(9):5479–5489. doi: 10.1128/mcb.13.9.5479. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Kerppola T. K. Fos and Jun bend the AP-1 site: effects of probe geometry on the detection of protein-induced DNA bending. Proc Natl Acad Sci U S A. 1996 Sep 17;93(19):10117–10122. doi: 10.1073/pnas.93.19.10117. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Kim J. L., Nikolov D. B., Burley S. K. Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature. 1993 Oct 7;365(6446):520–527. doi: 10.1038/365520a0. [DOI] [PubMed] [Google Scholar]
  14. Kim J., Zwieb C., Wu C., Adhya S. Bending of DNA by gene-regulatory proteins: construction and use of a DNA bending vector. Gene. 1989 Dec 21;85(1):15–23. doi: 10.1016/0378-1119(89)90459-9. [DOI] [PubMed] [Google Scholar]
  15. Landt O., Grunert H. P., Hahn U. A general method for rapid site-directed mutagenesis using the polymerase chain reaction. Gene. 1990 Nov 30;96(1):125–128. doi: 10.1016/0378-1119(90)90351-q. [DOI] [PubMed] [Google Scholar]
  16. Ma H. The unfolding drama of flower development: recent results from genetic and molecular analyses. Genes Dev. 1994 Apr 1;8(7):745–756. doi: 10.1101/gad.8.7.745. [DOI] [PubMed] [Google Scholar]
  17. Molkentin J. D., Black B. L., Martin J. F., Olson E. N. Cooperative activation of muscle gene expression by MEF2 and myogenic bHLH proteins. Cell. 1995 Dec 29;83(7):1125–1136. doi: 10.1016/0092-8674(95)90139-6. [DOI] [PubMed] [Google Scholar]
  18. Molkentin J. D., Black B. L., Martin J. F., Olson E. N. Mutational analysis of the DNA binding, dimerization, and transcriptional activation domains of MEF2C. Mol Cell Biol. 1996 Jun;16(6):2627–2636. doi: 10.1128/mcb.16.6.2627. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. 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]
  20. Nurrish S. J., Treisman R. DNA binding specificity determinants in MADS-box transcription factors. Mol Cell Biol. 1995 Aug;15(8):4076–4085. doi: 10.1128/mcb.15.8.4076. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Pellegrini L., Tan S., Richmond T. J. Structure of serum response factor core bound to DNA. Nature. 1995 Aug 10;376(6540):490–498. doi: 10.1038/376490a0. [DOI] [PubMed] [Google Scholar]
  22. 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]
  23. 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]
  24. Pontiggia A., Rimini R., Harley V. R., Goodfellow P. N., Lovell-Badge R., Bianchi M. E. Sex-reversing mutations affect the architecture of SRY-DNA complexes. EMBO J. 1994 Dec 15;13(24):6115–6124. doi: 10.1002/j.1460-2075.1994.tb06958.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Riechmann J. L., Krizek B. A., Meyerowitz E. M. Dimerization specificity of Arabidopsis MADS domain homeotic proteins APETALA1, APETALA3, PISTILLATA, and AGAMOUS. Proc Natl Acad Sci U S A. 1996 May 14;93(10):4793–4798. doi: 10.1073/pnas.93.10.4793. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Riechmann J. L., Wang M., Meyerowitz E. M. DNA-binding properties of Arabidopsis MADS domain homeotic proteins APETALA1, APETALA3, PISTILLATA and AGAMOUS. Nucleic Acids Res. 1996 Aug 15;24(16):3134–3141. doi: 10.1093/nar/24.16.3134. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Schultz S. C., Shields G. C., Steitz T. A. Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees. Science. 1991 Aug 30;253(5023):1001–1007. doi: 10.1126/science.1653449. [DOI] [PubMed] [Google Scholar]
  28. Sharrocks A. D. A T7 expression vector for producing N- and C-terminal fusion proteins with glutathione S-transferase. Gene. 1994 Jan 28;138(1-2):105–108. doi: 10.1016/0378-1119(94)90789-7. [DOI] [PubMed] [Google Scholar]
  29. 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]
  30. Sharrocks A. D., Shore P. DNA bending in the ternary nucleoprotein complex at the c-fos promoter. Nucleic Acids Res. 1995 Jul 11;23(13):2442–2449. doi: 10.1093/nar/23.13.2442. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. 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]
  32. Shaw P. E. Ternary complex formation over the c-fos serum response element: p62TCF exhibits dual component specificity with contacts to DNA and an extended structure in the DNA-binding domain of p67SRF. EMBO J. 1992 Aug;11(8):3011–3019. doi: 10.1002/j.1460-2075.1992.tb05371.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Shore P., Sharrocks A. D. The MADS-box family of transcription factors. Eur J Biochem. 1995 Apr 1;229(1):1–13. doi: 10.1111/j.1432-1033.1995.tb20430.x. [DOI] [PubMed] [Google Scholar]
  34. Shore P., Sharrocks A. D. The transcription factors Elk-1 and serum response factor interact by direct protein-protein contacts mediated by a short region of Elk-1. Mol Cell Biol. 1994 May;14(5):3283–3291. doi: 10.1128/mcb.14.5.3283. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Treisman R. The serum response element. Trends Biochem Sci. 1992 Oct;17(10):423–426. doi: 10.1016/0968-0004(92)90013-y. [DOI] [PubMed] [Google Scholar]
  36. Weigel D., Meyerowitz E. M. The ABCs of floral homeotic genes. Cell. 1994 Jul 29;78(2):203–209. doi: 10.1016/0092-8674(94)90291-7. [DOI] [PubMed] [Google Scholar]
  37. Werner M. H., Gronenborn A. M., Clore G. M. Intercalation, DNA kinking, and the control of transcription. Science. 1996 Feb 9;271(5250):778–784. doi: 10.1126/science.271.5250.778. [DOI] [PubMed] [Google Scholar]

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