A DISTINCT CLASS OF HOMEODOMAIN PROTEINS IS ENCODED BY 2 SEQUENTIALLYEXPRESSED DROSOPHILA GENES FROM THE 93D E CLUSTER/

Homeodomains appear to be one of the most frequently employed DNA-bind ing domains in a superfamily of transacting factors. It is likely that during evolution several sub-types of homeodomain have evolved from a common ancestral domain, resulting in distinct but closely related DN A-binding preferences. Here we describe the conservation of a distinct type of homeodomain encoded by the Drosophila lady-bird-late (lbl) ge ne, previously named nkch4 (1). Using degenerate PCR primers correspon ding to the most divergent regions of the first and third helix of the Lbl homeodomain we have amplified, from genomic DNA of the fly, a lad y-bird-like homeobox fragment. The Drosophila PCR products contained b oth the lbl (1) and a highly related homeobox sequence, which we named lady-bird-early (lbe). This new Drosophila gene resides directly upst ream to lbl and together with tinman/NK4 (2, 3, 4, 5), bagpipe/NK3 (2, 4) S59/NK1 (4, 6) and 93Bal (7) compose the 93D/E homeobox gene clust er. lbe and lbl are transcribed from the same strand and in a temporal order corresponding to their 5' -3' chromosomal location. Transcripts of both genes are found in the epiderm of Drosophila embryos, in cell s known to express a segment polarity gene wingless (8), and their spa tial and temporal colinearity of expression strongly suggests that the y cooperate during segmentation. The amino-acid composition of both La dy-bird homeodomains differ from that of Antp-type at several position s involved in DNA recognition. These substitutions appear to modify DN A-binding preferences since Lbl homeodomain is unable to recognize the most common homeodomain binding TAAT motif in gel retardation experim ents.