Recognition of Multiple Patterns of DNA Sites by Drosophila Homeodomain Protein Bicoidl

Abstract

Our previous studies demonstrated that the Drosophila homeodomain protein, Bicoid (Bed), binds DNA cooperatively. In this study, we determined the patterns of adjacent DNA sites required for cooperative recognition by Bed. Our in vitro selection and biochemical experiments demonstrated that Bcd binds preferentially to both head-to-head and tail-to-tail symmetric sites that are separated by short spacing. An increase in the spacing reduces the strict requirement of symmetric patterns of adjacent sites, permitting Bed to recognize tandem repeat sites cooperatively. Our further experiments in vivo showed that the only pair of optimally spaced symmetric Bed sites in a hunchback (hb) enhancer element contributes the most to transcriptional activation by Bed, demonstrating the biological importance of the binding site patterns revealed by our in vitro selection studies.