The homeodomain: an ancient evolutionary motif in animals and plants.

The homeodomain is a DNA-binding motif within transcription factor proteins. These transcription factors may be involved in cell differentiation and control of cell growth, as well as patterning of diverse organisms. Given their strong evolutionary conservation, it has been suggested that homeodomain proteins have been fundamental to the evolution of animal species. We have previously shown that the major classes of animal homeodomains originated early in the evolution of metazoans. Here, I investigate the evolutionary relationships of homeodomain sequences in plants. Using distance matrix approaches with unweighted or weighted character state transitions, the overall results support the same conclusion: in plants, as in animals, multiple independent classes of divergent homeodomains can be distinguished, again suggesting an early evolutionary origin. These studies advance the hypothesis that the homeodomain represents a fundamental motif of gene regulation in multicellular organisms.