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Optimal DNA sequence recognition by the Ultrabithorax homeodomain of Drosophila.
Author(s) -
Ekker S. C.,
Young K. E.,
Kessler D. P.,
Beachy P. A.
Publication year - 1991
Publication title -
the embo journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 7.484
H-Index - 392
eISSN - 1460-2075
pISSN - 0261-4189
DOI - 10.1002/j.1460-2075.1991.tb08058.x
Subject(s) - ultrabithorax , biology , homeobox , homeotic gene , binding site , genetics , transcription factor , hox gene , dna binding site , gene , consensus sequence , transcription (linguistics) , promoter , peptide sequence , gene expression , linguistics , philosophy
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 (KD approximately 7 × 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.