ArticleThe Journal of biological chemistry2008
Multiple intrinsically disordered sequences alter DNA binding by the homeodomain of the Drosophila hox protein ultrabithorax.
Article in The Journal of biological chemistry, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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38 citing papers in PubMed, 97 citations in OpenAlex.
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- Short activation domains control chromatin association of transcription factors.bioRxiv : the preprint server for biology · 2025Article
- Generation of Hoxa11-3XFLAG and Hoxd11-3XFLAG alleles to investigate Hox11 genome-wide binding.Developmental biology · 2025Article
- Biology of Hox Genes: Questions and Technological Challenges.Methods in molecular biology (Clifton, N.J.) · 2025Review
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- Hox genes in development and beyond.Development (Cambridge, England) · 2023Article
- Sequence Properties of An Intramolecular Interaction That Inhibits p53 DNA Binding.Biomolecules · 2022Article
- The unstructured linker of Mlh1 contains a motif required for endonuclease function which is mutated in cancers.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
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- Directed mutational scanning reveals a balance between acidic and hydrophobic residues in strong human activation domains.Cell systems · 2022Article
- Diversification and Functional Evolution of HOX Proteins.Frontiers in cell and developmental biology · 2022Review
- Transcription Factor Dynamics.Cold Spring Harbor perspectives in biology · 2021Review
- Dynamic Autoinhibition of the HMGB1 Protein via Electrostatic Fuzzy Interactions of Intrinsically Disordered Regions.Journal of molecular biology · 2021Article
- Physical Chemistry of the Protein Backbone: Enabling the Mechanisms of Intrinsic Protein Disorder.The journal of physical chemistry. B · 2020Review
- Multi-level and lineage-specific interactomes of the Hox transcription factor Ubx contribute to its functional specificity.Nature communications · 2020Article
- Thermodynamics of Conformational Transitions in a Disordered Protein Backbone Model.Biophysical journal · 2018Article
- Intrinsic Disorder and Posttranslational Modifications: The Darker Side of the Biological Dark Matter.Frontiers in genetics · 2018Review
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3 authors at 1 institution in 1 country.
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Abstract
During animal development, distinct tissues, organs, and appendages are specified through differential gene transcription by Hox transcription factors. However, the conserved Hox homeodomains bind DNA with high affinity yet low specificity. We have therefore explored the structure of the Drosophila melanogaster Hox protein Ultrabithorax and the impact of its nonhomeodomain regions on DNA binding properties. Computational and experimental approaches identified several conserved, intrinsically disordered regions outside the homeodomain of Ultrabithorax that impact DNA binding by the homeodomain. Full-length Ultrabithorax bound to target DNA 2.5-fold weaker than its isolated homeodomain. Using N-terminal and C-terminal deletion mutants, we demonstrate that the YPWM region and the disordered microexons (termed the I1 region) inhibit DNA binding approximately 2-fold, whereas the disordered I2 region inhibits homeodomain-DNA interaction a further approximately 40-fold. Binding is restored almost to homeodomain affinity by the mostly disordered N-terminal 174 amino acids (R region) in a length-dependent manner. Both the I2 and R regions contain portions of the activation domain, functionally linking DNA binding and transcription regulation. Given that (i) the I1 region and a portion of the R region alter homeodomain-DNA binding as a function of pH and (ii) an internal deletion within I1 increases Ultrabithorax-DNA affinity, I1 must directly impact homeodomain-DNA interaction energetics. However, I2 appears to indirectly affect DNA binding in a manner countered by the N terminus. The amino acid sequences of I2 and much of the I1 and R regions vary significantly among Ultrabithorax orthologues, potentially diversifying Hox-DNA interactions.
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