Faculty Bibliography

Many Drosophila developmental genes contain a DNA binding domain encoded by the homeobox. This homeodomain contains a region distantly homologous to the helix-turn-helix motif present in several prokaryotic DNA binding proteins. We investigated the nature of homeodomain-DNA interactions by making a series of mutations in the helix-turn-helix motif of the Drosophila homeodomain protein Paired (Prd). This protein does not recognize sequences bound by the homeodomain proteins Fushi tarazu (Ftz) or Bicoid (Bcd). We show that changing a single amino acid at the C-terminus of the recognition helix is both necessary and sufficient to confer the DNA binding specificity of either Ftz or Bcd on Prd. This simple rule indicates that the amino acids that determine the specificity of homeodomains are different from those mediating protein-DNA contacts in prokaryotic proteins. We further show that Prd contains two DNA binding activities. The Prd homeodomain is responsible for one of them while the other is not dependent on the recognition helix.

The first zygotic genes to be expressed during early Drosophila development are the gap genes. Their role is to read and interpret coarse positional information deposited in the egg by the mother and to refine it by cross-regulatory interactions and by controlling a class of pair-rule genes. Little is known about the molecular mechanisms by which the three cloned gap genes carry out their genetically defined functions. Here we report that the Kruppel (Kr) gene product (Kr) binds to the sequence AAGGGGTTAA, whereas the hunchback (hb) gene product (Hb) recognizes the consensus ACNCAAAAAANTA. We have identified binding sites for these proteins upstream of the two hb promoters, which we suggest could mediate the repression of hb by Kr and perhaps allow hb to influence its own expression.