Optimal DNA sequence recognition by the Ultrabithorax homeodomain of Drosophila

S. C. Ekker, K. E. Young, D. P. Von Kessler, P. A. Beachy

Research output: Contribution to journalArticle

130 Scopus citations

Abstract

The 61 amino acid homeodomain is conserved among members of a family of eukaryotic DNA-binding proteins that play regulatory roles in transcription and in development. We have refined a rapid method for determining optimal DNA binding sites and have applied it to a 72 amino acid peptide containing the homeodomain of the Ultrabithorax (Ubx) homeotic gene of Drosophila. The site (5'-TTAATGG-3') is tightly bound (K(D) ~7 x 10-11 M) by the Ubx homeodomain peptide; the four central TAAT bases of this sequence play a primary role in determining the affinity of binding, with significant secondary contributions deriving from the flanking bases. Although previously defined genomic sites contain multiple TAAT sequences with flanking bases distinct from those in the optimal binding site, we have found a new binding site with seven near-perfect repeats of the optimal sequence; this site is located in the promoter region of decapentaplegic, a probable Ubx regulatory target. The presence of a TAAT motif in the binding sites for most other homeodomain proteins suggests the existence of a conserved mechanism for recognition of this core sequence, with further specificity conferred by interactions with bases flanking this core.

Original languageEnglish (US)
Pages (from-to)1179-1186
Number of pages8
JournalEMBO Journal
Volume10
Issue number5
DOIs
StatePublished - Jan 1 1991

Keywords

  • DNA recognition
  • Drosophila
  • Ultrabithorax
  • development
  • homeodomain

ASJC Scopus subject areas

  • Neuroscience(all)
  • Molecular Biology
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)

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