Albany 2013: Book of Abstracts

category image Albany 2013
Conversation 18
June 11-15 2013
©Adenine Press (2012)

Generating context-specific functions with intrinsically disordered domains

Like many transcription factors important for animal development, members of the Hox protein family instigate multiple tissue-specific developmental programs. In each tissue, an individual Hox protein regulates a different subset of gene targets. Consequently, Hox proteins must sense positional information from the cell and select different DNA binding targets in response. Furthermore, Hox proteins must sense which gene it has bound and select which mode of transcription regulation – activation or repression – to implement at each site. Our studies with the Drosophila Hox protein Ultrabithorax (Ubx) in vitro and in vivo demonstrate that interplay between intramolecular and intermolecular protein interactions involving intrinsically disordered regions play key roles in these sense-and-select mechanisms. The Ubx protein comprises a structured DNA-binding homeodomain, which accounts for ~15% of the protein, short elements with predicted helical structure, and two large intrinsically disordered regions. Most of the protein sequence influences DNA binding affinity by the homeodomain. The two intrinsically disordered regions directly contact the homeodomain and impact DNA binding specificity as well. Consequently, protein interaction regions, alternatively spliced sequences, and phosphorylation sites embedded within these disordered regions provide an opportunity for cellular events to modulate DNA binding. In particular, the C-terminal intrinsically disordered region appears to act as a tissue identity sensor. This region consists of a binding motif for the Hox cofactor Exd, separated from the homeodomain by alternatively spliced disordered segments. Intramolecular interactions allow the motif to prevent monomer binding to Ubx-Exd composite sequences. As the distance between the motif and the homeodomain is shortened by splicing, DNA binding by Ubx monomers and multimers is inhibited as well. Tissue identity determines both Exd availability and the identity of the Ubx splicing isoform, which together dictates which subset of Ubx target sequences is bound: high affinity monomer sites, low affinity monomer sites, and/or Ubx-Exd heterodimer sites. The N-terminal disordered region binds transcription factors that subdivide Ubx-specified tissues, and thus may transmit positional information within the tissue to the homeodomain. Conversely, DNA binding triggers a large conformational change in Ubx which exposes these intrinsically disordered regions to solvent. This conformational change in Ubx varies with the DNA sequence bound, providing a mechanism for the DNA sequence to influence protein interactions and transcription regulation. The reciprocal nature of these interactions reinforces and stabilizes “correct” Ubx-DNA complexes, generating the reliability that is a necessary part of Hox function.


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  3. Y. Liu, K.S. Matthews, & S.E. Bondos (2008) Multiple intrinsically disordered sequences alter DNA binding by the homeodomain of the Droosphila Hox protein Ultrabithorax. J. Biol. Chem. 283, 20874-20887.
  4. S.E. Bondos, X.X. Tan, K.S. Matthews (2006) Physical and genetic interactions link Hox function with diverse transcription factors and cell signaling proteins. Mol. Cell Proteomics 5, 824-834.

Ying Liu1,2
Kathleen S. Matthews2
and Sarah E. Bondos1,2

1Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77005
2Department of Molecular and Cellular Medicine, Texas A&M Health Science Center College Station, TX 77845-1114

Ph: (979) 845-5399
Fx: (979) 847-9481
Email: sebondos@tamhsc.edu