Functional Specificity of a Hox Protein Mediated by the Recognition of Minor Groove Structure

Joshi, Rohit; Passner, J.M.; Rohs, Remo; Jain, Rinku; Sosinsky, Alona; Crickmore, Michael A.; Jacob, Vinitha; Aggarwal, Aneel K.; Honig, Barry; Mann, Richard S.

doi:10.1016/j.cell.2007.09.024

Cited by 318 publications

(510 citation statements)

References 60 publications

(89 reference statements)

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“…In all four structures the trajectory of the DNA backbone deviates from B-form DNA at the core GA base step within the Exd/Pbx1 binding site. This base step is critical for Exd/Pbx1 binding as observed in the crystal structure (32)(33)(34)(35) as well as our own comprehensive CSI microarray studies (46).…”

Section: Dna Groove Dimensions In Hox-exd/pbx1 Structuresmentioning

confidence: 74%

“…The premise is further supported by the fact that simply decreasing conformational flexure of the Exd binding site, as would happen as a result of polyamide binding in the Inverse register, does not enhance binding to the same degree as it does when the Dp tail is in close proximity of the GA base step. The effect of minor groove located charges in Hox-three amino acid loop extension homeodomain (TALE) complexes has been borne out in structural studies of Scr-Exd-DNA complexes, where a minor groove bound arginine from Scr has been correlated with allosteric Scr-Exd interactions (35). However the studies with Scr posited that this effect was due to pre-existing DNA conformational preferences between different DNAs.…”

Section: Rationale For the Allosteric Effectmentioning

confidence: 99%

“…Most of this cooperative interaction is the result of a conserved N-terminal YPWM tetrapeptide on the Hox protein binding into a pocket on the Exd/Pbx1 homeodomain ( Figure 1, panel a). In addition to this direct interface between Hox and Exd/Pbx1, crystal structures of four Hox-Exd/Pbx1-DNA complexes reveal a discernible perturbation of DNA geometry in the ternary complex (32)(33)(34)(35). Importantly, there is compelling evidence that Hox-Exd-DNA complex may not require interaction between the Hox N-terminal docking peptide and Exd (28,36).…”

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confidence: 99%

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Targeted Chemical Wedges Reveal the Role of Allosteric DNA Modulation in Protein−DNA Assembly

et al. 2008

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The cooperative assembly of multiprotein complexes results from allosteric modulations of DNA structure as well as direct intermolecular contacts between proteins. Such cooperative binding plays a critical role in imparting exquisite sequence specificity on the homeobox transcription factor (Hox) family of developmental transcription factors. A well-characterized example includes the interaction of Hox proteins with extradenticle (Exd), a highly conserved DNA binding transcription factor. Although direct interactions are important, the contribution of indirect interactions toward cooperative assembly of Hox and Exd remains unresolved. Here we use minor groove binding polyamides as structural wedges to induce perturbations at specific base steps within the Exd binding site. We find that allosteric modulation of DNA structure contributes nearly 1.5 kcal/mol to the binding of Exd to DNA, even in the absence of direct Hox contacts. In contrast to previous studies, the sequence-targeted chemical wedges reveal the role of DNA geometry in cooperative assembly of Hox-Exd complexes. Programmable polyamides may well serve as general probes to investigate the role of DNA modulation in the cooperative and highly specific assembly of other protein-DNA complexes.The physical basis of DNA sequence recognition by its ligands (proteins or small molecules) has been investigated in great detail over the years, and several underlying principles have been defined (1-3). The main contributors to the specificity of DNA sequence recognition are interactions between protein side chains and the edges of the base pairs in the cognate DNA site. Efforts to rationally redesign these direct interactions have yielded some exciting successes (4-8). A major limitation of focusing on re-engineering direct interactions, however, is that recognition of sequence-dependent structural properties of DNA and other modes of indirect readout are also critical specificity determinants (9-15). Often a combination of direct and indirect interactions governs exquisite DNA sequence specificity displayed by its ligands (9,11,(14)(15)(16)(17)(18)(19)(20)(21)(22). Specificity in molecular recognition is also achieved by cooperative binding of multiple proteins to closely appositioned DNA sequences (23). Binding of one protein to its DNA cognate site in the enhancer can alter DNA structure and conformational flexibility of a juxtaposed site, thus allosterically improving the energetics

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Section: Dna Groove Dimensions In Hox-exd/pbx1 Structuresmentioning

confidence: 74%

Section: Rationale For the Allosteric Effectmentioning

confidence: 99%

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confidence: 99%

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Targeted Chemical Wedges Reveal the Role of Allosteric DNA Modulation in Protein−DNA Assembly

et al. 2008

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“…The discovery of Exd/Hth cofactors conferring additional specificity provided one new element of response (9). Also, the spacing specific residues located in the N-terminal arm of the HD also contribute to Hox specificity (25). Other nuclear partners, generating different combinations of HOX transcription factor complexes integrating a variety of positional cues, generate the specificity and versatility required for context-dependent Hox function (8,(25)(26)(27)(28).…”

Section: Discussionmentioning

confidence: 99%

Cross-regulatory protein–protein interactions between Hox and Pax transcription factors

Plaza

Prince

Adachi

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

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Homeotic Hox selector genes encode highly conserved transcriptional regulators involved in the differentiation of multicellular organisms. Ectopic expression of the Antennapedia (ANTP) homeodomain protein in Drosophila imaginal discs induces distinct phenotypes, including an antenna-to-leg transformation and eye reduction. We have proposed that the eye loss phenotype is a consequence of a negative posttranslational control mechanism because of direct protein-protein interactions between ANTP and Eyeless (EY). In the present work, we analyzed the effect of various ANTP homeodomain mutations for their interaction with EY and for head development. Contrasting with the eye loss phenotype, we provide evidence that the antenna-to-leg transformation involves ANTP DNA-binding activity. In a complementary genetic screen performed in yeast, we isolated mutations located in the N terminus of the ANTP homeodomain that inhibit direct interactions with EY without abolishing DNA binding in vitro and in vivo. In a bimolecular fluorescence complementation assay, we detected the ANTP-EY interaction in vivo, these interactions occurring through the paired domain and/or the homeodomain of EY. These results demonstrate that the homeodomain supports multiple molecular regulatory functions in addition to protein-DNA and protein-RNA interactions; it is also involved in protein-protein interactions. Drosophila ͉ antagonism ͉ regulation H omeotic Hox genes are selector genes that generate morphological diversity along the antero-posterior body axis during animal development (1). They encode highly conserved transcription factors defining various cellular identities in the body segments along the antero-posterior axis of the embryo (2, 3). Hox genes share a common sequence element of 180 bp, the homeobox, first isolated in Drosophila (4, 5), encoding a 60-aa homeodomain (HD) DNA-binding domain. The HD presents a stereotypical three ␣-helical structure, and its mode of interaction with DNA is largely invariant. The amino acid 50, a glutamine signature for the Hox proteins, plays a fundamental role in DNA-binding specificity (6). Hox factors have very similar DNA-binding properties (7). Therefore, the limited sequence selectivity of the HD is not sufficient to explain the diversity of cell types and the batteries of downstream genes under the control of Hox proteins. Consequently, elucidating the mechanisms of Hox protein function is critical for understanding development and the diversification of serially homologous structures. Several studies have indicated that Hox factors cooperate with signaling pathways and act with cofactors that modify DNA binding and activation/repression properties (8-10). To date, the best-known Hox cofactors are the Drosophila extradenticle (EXD/PBX) and homothorax (HTH/Meis) proteins. EXD was shown to modulate the DNA-binding specificity and the activity of Hox proteins (11-13), whereas HTH promotes EXD translocation into the nucleus where they participate in a DNA-bound HOX/EXD/HTH ternary complex (14). Altho...

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“…More recent studies have revealed that the specific regulation of fork head (fkh) by Sex combs reduced (Scr) occurs through the recognition of a specific DNA structure that is itself dependent on the nucleotide sequence [16]. Using a high throughput approach based on systematic evolution of ligands by exponential enrichment and massively parallel sequencing (SELEX-seq) to define preferential DNA-binding sites, it was shown that this mode of recognition also applied to all other Drosophila Hox/PBC complexes [10].…”

Section: Introductionmentioning

confidence: 99%

Hox transcriptional specificity despite a single class of cofactors: Are flexible interaction modes the key?

Merabet

Hudry

2012

BioEssays

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Editor's suggested further reading in BioEssays ftz Evolution: Findings, hypotheses and speculations (response to DOI 10.1002/bies.201100019) AbstractOn the border of the homeotic function: Re‐evaluating the controversial role of cofactor‐recruiting motifs AbstractControl of DNA replication: A new facet of Hox proteins? AbstractClassification of sequence signatures: a guide to Hox protein function Abstract

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Functional Specificity of a Hox Protein Mediated by the Recognition of Minor Groove Structure

Cited by 318 publications

References 60 publications

Targeted Chemical Wedges Reveal the Role of Allosteric DNA Modulation in Protein−DNA Assembly

Targeted Chemical Wedges Reveal the Role of Allosteric DNA Modulation in Protein−DNA Assembly

Cross-regulatory protein–protein interactions between Hox and Pax transcription factors

Hox transcriptional specificity despite a single class of cofactors: Are flexible interaction modes the key?

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