Analysis of Usp DNA binding domain targeting reveals critical determinants of the ecdysone receptor complex interaction with the response element

We have used circular permutation analysis to determine whether binding of purified Xenopus laevis estrogen receptor DNA-binding domain (DBD) to a DNA fragment containing an estrogen response element (ERE) causes the DNA to bend. Gel mobility shift assays showed that DBD-DNA complexes formed with fragments containing more centrally located EREs migrated more slowly than complexes formed with fragments containing EREs near the ends of the DNA. DNA bending standards were used to determine that the degree of bending induced by binding of the DBD to an ERE was approximately 34 degrees. A 1.55-fold increase in the degree of bending was observed when two EREs were present in the DNA fragment. These in vitro studies suggest that interaction of nuclear receptors with their hormone response elements in vivo may result in an altered DNA conformation.

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Designing of RNA aptamer against DNA binding domain of the glucocorticoid receptor: A response element-based in-silico approach

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2020.1822918 ◽

2020 ◽

pp. 1-8

Author(s):

Thirukumaran Kandasamy ◽

Babu Sudhamalla ◽

Debdut Naskar

Keyword(s):

Dna Binding ◽

Glucocorticoid Receptor ◽

In Silico ◽

Binding Domain ◽

Rna Aptamer ◽

Dna Binding Domain ◽

Response Element

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Proton NMR studies of DNA recognition by the glucocorticoid receptor: complex of the DNA binding domain with a half-site response element

Biochemistry ◽

10.1021/bi00114a003 ◽

1991 ◽

Vol 30 (50) ◽

pp. 11620-11624 ◽

Cited By ~ 14

Author(s):

M. L. Remerowski ◽

E. Kellenbach ◽

R. Boelens ◽

G. A. Van der Marel ◽

J. H. Van Boom ◽

...

Keyword(s):

Dna Binding ◽

Glucocorticoid Receptor ◽

Site Response ◽

Dna Recognition ◽

Proton Nmr ◽

Receptor Complex ◽

Dna Binding Domain ◽

Nmr Studies ◽

Response Element ◽

Half Site

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DNA recognition by the androgen receptor: evidence for an alternative DNA-dependent dimerization, and an active role of sequences flanking the response element on transactivation

Biochemical Journal ◽

10.1042/bj20020912 ◽

2003 ◽

Vol 369 (1) ◽

pp. 141-151 ◽

Cited By ~ 41

Author(s):

Annemie HAELENS ◽

Guy VERRIJDT ◽

Leen CALLEWAERT ◽

Valerie CHRISTIAENS ◽

Kris SCHAUWAERS ◽

...

Keyword(s):

Androgen Receptor ◽

Dna Binding ◽

Steroid Receptors ◽

Binding Domain ◽

Hinge Region ◽

General Mechanism ◽

Affinity Binding ◽

Dna Binding Domain ◽

Direct Repeats ◽

Response Element

The androgen receptor has a subset of target DNA sequences, which are not recognized by any other steroid receptors. The androgen selectivity of these sequences was proposed to be the consequence of the ability of the androgen receptor to dimerize on direct repeats of 5′-TGTTCT-3′-like sequences. This is in contrast with the classical non-selective elements consisting of inverted repeats of the 5′-TGTTCT-3′ elements separated by three nucleotides and which are recognized by other steroid receptors in addition to the androgen receptor. We demonstrate that while the DNA-binding domain of the oestrogen receptor is unable to dimerize on direct repeats, dimeric binding can be rescued by replacing the second Zn finger and part of the hinge region by the corresponding fragment of the androgen receptor, but not the glucocorticoid receptor. In this study, we investigate the androgen receptor binding to all natural androgen-selective response elements described so far. We show that a 12-amino acid C-terminal extension of the DNA-binding domain is required for high-affinity binding of the androgen receptor to all these elements. For one androgen-specific low-affinity binding site, the flanking sequences do not contribute to the invitro affinity of the androgen receptor DNA-binding domain. Surprisingly, however, they control the transcriptional activity of the androgen receptor in transient transfection experiments. In conclusion, we give evidence that the alternative DNA-dependent dimerization of the androgen receptor on direct repeats is a general mechanism for androgen specificity in which the second Zn finger and hinge region are involved. In addition, the sequences flanking an androgen-response element can control the activity of the androgen receptor.

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Two domains of ISGF3 gamma that mediate protein-DNA and protein-protein interactions during transcription factor assembly contribute to DNA-binding specificity.

Molecular and Cellular Biology ◽

10.1128/mcb.13.1.196 ◽

1993 ◽

Vol 13 (1) ◽

pp. 196-206 ◽

Cited By ~ 86

Author(s):

S A Veals ◽

T Santa Maria ◽

D E Levy

Keyword(s):

Amino Acids ◽

Transcription Factor ◽

Dna Binding ◽

Protein Interaction ◽

Binding Specificity ◽

Binding Domain ◽

Dna Binding Domain ◽

Response Element ◽

Ifn Alpha ◽

Dna Binding Specificity

Alpha interferon (IFN-alpha) induces the transcription of a large set of genes through activation of multimeric transcription factor ISGF3. This factor can be dissociated into two protein components, termed ISGF3 gamma and ISGF3 alpha. ISGF3 gamma is a 48-kDa protein related at the amino terminus to members of the IFN-regulatory factor (IRF) and Myb families of DNA-binding proteins; ISGF3 alpha consists of three polypeptides of 84, 91, and 113 kDa that self-assemble to form an activated component in response to IFN-alpha. DNA-binding studies indicated that ISGF3 gamma binds DNA alone, recognizing the IFN-stimulated response element, while the ISGF3 alpha polypeptides alone display no specific interactions with DNA. A complex between ISGF3 gamma and activated ISGF3 alpha binds the IFN-stimulated response element with much greater affinity than does the 48-kDa ISGF3 gamma protein alone. The DNA-binding domain of ISGF3 gamma and regions responsible for protein-protein interaction with ISGF3 alpha were identified by using deleted forms of ISGF3 gamma expressed in vitro. The amino-terminal region of ISGF3 gamma homologous to the IRF and Myb proteins was sufficient for interaction with DNA and displayed the binding specificity of the intact protein; phosphorylation of this region was necessary for activity. A second region of 160 amino acids separated from the DNA-binding domain by over 100 amino acids contained a domain capable of associating with ISGF3 alpha and was sufficient to confer specific ISGF3 alpha interaction to a heterologous protein. Interaction of the ISGF3 alpha component with the protein interaction domain of ISGF3 gamma altered the DNA-binding specificity of the resulting complex, suggesting that one or more of the ISGF3 alpha polypeptides make base-specific contacts with DNA. This interaction defines a mechanism through which IRF-like proteins complexed with regulatory components can display novel DNA-binding specificities.

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Equilibrium Analysis of the DNA Binding Domain of the Ultraspiracle Protein Interaction with the Response Element from the hsp27 Gene Promoter—the Application of Molecular Beacon Technology

Journal of Fluorescence ◽

10.1007/s10895-007-0285-y ◽

2007 ◽

Vol 18 (1) ◽

pp. 1-10 ◽

Cited By ~ 4

Author(s):

Tomasz Krusiński ◽

Marta Wietrzych ◽

Iwona Grad ◽

Andrzej Ożyhar ◽

Piotr Dobryszycki

Keyword(s):

Dna Binding ◽

Protein Interaction ◽

Molecular Beacon ◽

Gene Promoter ◽

Binding Domain ◽

Equilibrium Analysis ◽

Dna Binding Domain ◽

Response Element

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Constitutively active FOXO1a and a DNA-binding domain mutant exhibit distinct co-regulatory functions to enhance progesterone receptor A activity

Journal of Molecular Endocrinology ◽

10.1677/jme-07-0017 ◽

2007 ◽

Vol 38 (6) ◽

pp. 673-690 ◽

Cited By ~ 12

Author(s):

Michael D Rudd ◽

Ignacio Gonzalez-Robayna ◽

Inmaculada Hernandez-Gonzalez ◽

Nancy L Weigel ◽

William E Bingman ◽

...

Keyword(s):

Transcription Factors ◽

Dna Binding ◽

Hormone Receptors ◽

Binding Domain ◽

Nuclear Hormone Receptors ◽

Dna Binding Domain ◽

Transactivation Domain ◽

Response Element ◽

Regulatory Functions ◽

Constitutively Active

FOXO (Forkhead box O1 transcription factors) factors interact with and modify the activity of other transcription factors, including nuclear hormone receptors. However, not all of the structural domains within the FOXO proteins that mediate these functional interactions have been clearly defined. To address this issue, we used a constitutively active (nuclear) mutant of FOXO1a (designated FOXOA3) and within FOXOA3 made additional mutations to alter the putative nuclear hormone interacting domain (NID), minimal activation domain (MAD), DNA-binding domain (DBD), and the N terminus. We document that FOXOA3 enhanced the hormone-dependent transcriptional activity of liganded progesterone receptors A (PGRA) on a glucocorticoid response element-responsive promoter, PGRA on the insulin-like growth factor-binding protein 1 promoter, and estrogen receptor α on an estrogen response element-responsive promoter. The effects of FOXOA3 on PGRA were dependent, in part, on an intact NID, the MAD, and N-terminal domain. In striking contrast, a FOXOA3 DNA-binding mutant (FOXOA3-mDBD) modulated PGRA, PGRB, and ESR1 activities by distinctly different mechanisms, markedly elevating ligand-independent activity of these nuclear hormone receptors even in the double mutant lacking the MAD. Furthermore, both FOXOA3 and FOXOA3-mDBD enhanced the activity of a transcriptionally defective PGRA lacking its AF1 transactivation domain, indicating that this region of the receptor is not essential in this context. Since FOXOA3, FOXOA3-mDBD, and FOXOA3-mNID all bound PGRA in a GST pull-down assay, it appears that the LXXLL (leucine–X–X–leucine–leucine) motif within the NID is not critical for FOXOA3 interactions with PGRA, but may modify the recruitment of other co-regulatory molecules. Collectively, the results show that FOXOA3 exerts co-regulatory functions independent of DNA binding and that the DNA-binding defective form of FOXO1a is transcriptionally active as a co-regulator of these nuclear hormone receptors.

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