Evolution of the Intrinsically Disordered Activation Domain in a Hox Transcription Factor

Abstract

Linking changes in the amino acid sequence to the evolution of transcription regulatory domains is often complicated by the low sequence complexity and high mutation rates of intrinsically disordered protein regions. For the Hox transcription factor Ultrabithorax (Ubx), conserved motifs distributed throughout the protein sequence enable direct comparison of specific protein regions, despite variations in the length and composition of the intervening sequences. The Drosophila melanogaster Ubx transcription activation domain can be subdivided into an “enhancer region” that increases activation efficacy and a “core region” required for activation. In cell culture, the strength of transcription activation by Drosophila Ubx correlates with the presence of a predicted helix within the core region. Mutations in this helix alter Ubx activity in the developing wing, demonstrating its functional importance in vivo. Curiously, this helix is not preserved in species more divergent than flies, suggesting the nature of transcription activation may have evolved in these Ubx orthologues. A yeast one-hybrid assay demonstrated that the ability of full-length Ubx orthologues to activate transcription varies substantially in Ubx orthologues representing 540 million years of evolution. The sequence compositions and the locations of the activation domains also differ. Furthermore, the function of analogous regions of the Ubx protein may vary from being required for transcription activation, enhancing activation efficiency, having no activity, or even inhibiting transcription activation. We conclude that, unlike homeodomain-DNA binding, the nature of transcription activation by Ubx has substantially evolved.