Source: The Interactive Fly (http://sdb.bio.purdue.edu/fly/aimain/1aahome.htm).

Several of the gap genes encode zinc finger proteins, whereas genes such as the dorsovent-ral patterning gene twist and the pair-rule segmentation gene hairy encode basic HLH proteins. The identification of these DNA-binding motifs in proteins has allowed biologists to deduce the biochemical function of a gene product by inspecting its encoded sequence, rather than resorting to exhaustive biochemical analysis. Furthermore, because these motifs are involved in contact with DNA, they are often constrained with respect to evolutionary changes in their sequence. As a result, these highly conserved motifs are useful for isolating gene homologs in other taxa.

The second major category of toolkit genes encode proteins involved in the process of cell signaling, either as ligands, receptors for ligands, or components involved in the intracellular transduction of signals. At least seven major signaling pathways operate in the Drosophila embryo: the Hedgehog, Notch, Wingless, Dpp/transforming growth factor-P (TGF-P), Toll, epidermal growth factor (EGF), and fibroblast growth factor (FGF) signaling pathways (Table 2.2).

All of these pathways have similar elements—namely, each has at least one signaling ligand, at least one receptor spanning the cell membrane, and at least one DNA-binding transcription factor that responds to signaling inputs by binding to target genes to turn them on or off (Fig. 2.20). Although the signaling logic may be similar among pathways, the biochemistry is not. Many structural types of ligands and receptors exist, and each pathway regulates the activity of different transcription factors. The response to ligand binding is mediated by a variety of mechanisms that often involve post-translation modifications (for example, protein phosphorylation, proteolysis, binding to a cofactor) that regulate the activity of, or the translocation of, transcription factors to the cell nucleus (Fig. 2.20). The similar mutant phenotypes of some developmental genes reflect their involvement in the same signaling pathway. Any loss of a signaling ligand, receptor, or member of the signal transduction machinery can cause the pathway to fail.

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