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Internal regulatory interactions determine DNA binding specificity by a Hox transcription factor
Ying Liu1, Kathleen S Matthews, Sarah E Bondos
1Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77005, USA.
Journal of Molecular Biology
|June 2, 2009
Summary
Regions outside the Hox homeodomain, like the I1 region in Ultrabithorax Ia (UbxIa), significantly enhance DNA binding specificity. This network of interactions diversifies gene regulation by Hox proteins.
Area of Science:
- Developmental Biology
- Genetics
- Molecular Biology
Background:
- Hox transcription factors are crucial for body plan development in bilaterians.
- Hox homeodomains bind DNA, but full-length proteins exhibit greater sequence specificity in vivo.
- Regions outside the homeodomain are hypothesized to mediate this specificity.
Purpose of the Study:
- To investigate how regions outside the homeodomain of the Hox protein Ultrabithorax Ia (UbxIa) contribute to DNA binding specificity.
- To determine the role of the I1 region and its sub-segments in modulating UbxIa DNA interactions.
Main Methods:
- Comparative DNA binding affinity assays using isolated Ubx homeodomain (UbxHD) versus full-length UbxIa.
- Analysis of DNA binding specificity by examining affinity for disparate DNA sequences.
- Site-directed mutagenesis to probe the function of specific regions within the I1 domain, including the YPWM motif.
Main Results:
- Full-length UbxIa exhibits significantly higher DNA binding specificity ( >10-fold affinity difference) compared to UbxHD (<3-fold).
- The I1 region, particularly its sub-segments including the YPWM motif, is critical for enhancing UbxIa DNA specificity.
- The YPWM motif's function is context-dependent, inhibiting heterodimer binding sites but potentially also Hox-only sites when flanking regions are removed.
Conclusions:
- Non-homeodomain regions, like the I1 region, form a regulatory network that refines Hox protein DNA binding specificity.
- This network allows for context- and gene-specific regulation, diversifying the function of highly homologous Hox homeodomains.
- These findings highlight the importance of modular protein design and interaction networks in developmental gene regulation.
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