scholarly journals DNA-Binding Domain of AtTRB2 Reveals Unique Features of a Single Myb Histone Protein Family that Binds to Both Arabidopsis- and Human-Type Telomeric DNA Sequences

2012 ◽  
Vol 5 (6) ◽  
pp. 1406-1408 ◽  
Author(s):  
Won Kyung Lee ◽  
Ji-Hye Yun ◽  
Weontae Lee ◽  
Myeon Haeng Cho
Keyword(s):  
Dna Binding ◽  
Dna Sequences ◽  
Protein Family ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Telomeric Dna ◽  
Histone Protein ◽  
Human Type

scholarly journals The Crystal Structure of the DNA-Binding Domain of Yeast RAP1 in Complex with Telomeric DNA

Cell ◽  
1996 ◽  
Vol 85 (1) ◽  
pp. 125-136 ◽  
Author(s):  
Peter König ◽  
Rafael Giraldo ◽  
Lynda Chapman ◽  
Daniela Rhodes
Keyword(s):  
Crystal Structure ◽  
Dna Binding ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Telomeric Dna

scholarly journals Mechanism underlying the DNA-binding preferences of the Vibrio cholerae and vibriophage VP882 VqmA quorum-sensing receptors

2021 ◽  
Author(s):  
Bonnie L. Bassler ◽  
Olivia Duddy ◽  
Xiuliang Huang ◽  
Justin Silpe
Keyword(s):  
Dna Binding ◽  
Quorum Sensing ◽  
Vibrio Cholerae ◽  
Dna Sequences ◽  
Genetic Screen ◽  
Binding Domain ◽  
Communication Process ◽  
Dna Binding Domain ◽  
Phage Gene ◽  
Small Regulatory Rna

Quorum sensing is a chemical communication process that bacteria use to coordinate group behaviors. In the global pathogen Vibrio cholerae, one quorum-sensing receptor and transcription factor, called VqmA (VqmAVc), activates expression of the vqmR gene encoding the small regulatory RNA VqmR, which represses genes involved in virulence and biofilm formation. Vibriophage VP882 encodes a VqmA homolog called VqmAPhage that activates transcription of the phage gene qtip, and Qtip launches the phage lytic program. Curiously, VqmAPhage can activate vqmR expression but VqmAVc cannot activate expression of qtip. Here, we investigate the mechanism underlying this asymmetry. We find that promoter selectivity is driven exclusively by each VqmA DNA-binding domain and key DNA sequences in the vqmR and qtip promoters are required to maintain specificity. A protein sequence-guided mutagenesis approach revealed that the residue E194 of VqmAPhage and A192, the equivalent residue in VqmAVc, in the helix-turn-helix motifs contribute to promoter-binding specificity. A genetic screen to identify VqmAPhage mutants that are incapable of binding the qtip promoter but maintain binding to the vqmR promoter delivered additional VqmAPhage residues located immediately C-terminal to the helix-turn-helix motif as required for binding the qtip promoter. Surprisingly, these residues are conserved between VqmAPhage and VqmAVc. A second, targeted genetic screen revealed a region located in the VqmAVc DNA-binding domain as necessary to prevent VqmAVc from binding the qtip promoter, thus restricting DNA-binding to the vqmR promoter. We propose that the VqmAVc helix-turn-helix motif and the C-terminal flanking residues function together to prohibit VqmAVc from binding the qtip promoter.

scholarly journals Basis of Specificity in Ets-1 DNA Binding Domain to Variable DNA Sequences

2019 ◽  
Vol 116 (3) ◽  
pp. 486a
Author(s):  
Kenneth Huang ◽  
Suela Xhani ◽  
Amanda V. Albrecht ◽  
Gregory M.K. Poon
Keyword(s):  
Dna Binding ◽  
Dna Sequences ◽  
Binding Domain ◽  
Dna Binding Domain

DNA recognition by nuclear receptors

2004 ◽  
Vol 40 ◽  
pp. 59-72 ◽  
Author(s):  
Frank Claessens ◽  
Daniel T Gewirth
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Nuclear Receptors ◽  
Dna Sequences ◽  
Dna Recognition ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Core Motif ◽  
Response Elements ◽  
Sequence Recognition

The nuclear receptors constitute a large family of ligand-inducible transcription factors. The control of many genetic pathways requires the assembly of these nuclear receptors in defined transcription-activating complexes within control regions of ligand-responsive genes. An essential step is the interaction of the receptors with specific DNA sequences, called hormone-response elements (HREs). These response elements position the receptors, and the complexes recruited by them, close to the genes of which transcription is affected. HREs are bipartite elements that are composed of two hexameric core half-site motifs. The identity of the response elements resides in three features: the nucleotide sequence of the two core motif half-sites, the number of base pairs separating them and the relative orientation of the motifs. The DNA-binding domains of nuclear receptors consist of two zinc-nucleated modules and a C-terminal extension. Residues in the first module determine the specificity of the DNA recognition, while residues in the second module are involved in dimerization. Indeed, nuclear receptors bind to their HREs as either homodimers or heterodimers. Depending on the type of receptor, the C-terminal extension plays a role in sequence recognition, dimerization, or both. The DNA-binding domain is furthermore involved in several other functions including nuclear localization, and interaction with transcription factors and co-activators. It is also the target of post-translational modifications. The DNA-binding domain therefore plays a central role, not only in the correct binding of the receptors to the target genes, but also in the control of other steps of the action mechanism of nuclear receptors.

scholarly journals Sequence-Specific Deoxyribonucleic Acid (DNA) Recognition by Steroidogenic Factor 1: A Helix at the Carboxy Terminus of the DNA Binding Domain Is Necessary for Complex Stability

2006 ◽  
Vol 20 (4) ◽  
pp. 831-843 ◽  
Author(s):  
Tanya H. Little ◽  
Yongbo Zhang ◽  
Christina K. Matulis ◽  
Jennifer Weck ◽  
Zhipeng Zhang ◽  
...  
Keyword(s):  
Dna Binding ◽  
Dna Sequences ◽  
Hormone Receptors ◽  
Terminal Segment ◽  
Reproductive Hormones ◽  
Binding Domain ◽  
Proximal Promoter ◽  
Dna Binding Domain ◽  
Steroidogenic Factor 1 ◽  
The Core

Abstract Steroidogenic factor 1 (SF1) is a member of the NR5A subfamily of nuclear hormone receptors and is considered a master regulator of reproduction because it regulates a number of genes encoding reproductive hormones and enzymes involved in steroid hormone biosynthesis. Like other NR5A members, SF1 harbors a highly conserved approximately 30-residue segment called the FTZ-F1 box C-terminal to the core DNA binding domain (DBD) common to all nuclear receptors and binds to 9-bp DNA sequences as a monomer. Here we describe the solution structure of the SF1 DBD in complex with an atypical sequence in the proximal promoter region of the inhibin-α gene that encodes a subunit of a reproductive hormone. SF1 forms a specific complex with the DNA through a bipartite motif binding to the major and minor grooves through the core DBD and the N-terminal segment of the FTZ-F1 box, respectively, in a manner previously described for two other monomeric receptors, nerve growth factor-induced-B and estrogen-related receptor 2. However, unlike these receptors, SF1 harbors a helix in the C-terminal segment of the FTZ-F1 box that interacts with both the core DBD and DNA and serves as an important determinant of stability of the complex. We propose that the FTZ-F1 helix along with the core DBD serves as a platform for interactions with coactivators and other DNA-bound factors in the vicinity.

scholarly journals Functional Dissection of Human and Mouse POT1 Proteins

2008 ◽  
Vol 29 (2) ◽  
pp. 471-482 ◽  
Author(s):  
Wilhelm Palm ◽  
Dirk Hockemeyer ◽  
Tatsuya Kibe ◽  
Titia de Lange
Keyword(s):  
Dna Damage ◽  
Dna Binding ◽  
Dna Damage Response ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Telomeric Dna ◽  
C Terminus ◽  
Damage Response ◽  
End Resection

ABSTRACT The single-stranded telomeric DNA binding protein POT1 protects mammalian chromosome ends from the ATR-dependent DNA damage response, regulates telomerase-mediated telomere extension, and limits 5′-end resection at telomere termini. Whereas most mammals have a single POT1 gene, mice have two POT1 proteins that are functionally distinct. POT1a represses the DNA damage response, and POT1b controls 5′-end resection. In contrast, as we report here, POT1a and POT1b do not differ in their ability to repress telomere recombination. By swapping domains, we show that the DNA binding domain of POT1a specifies its ability to repress the DNA damage response. However, no differences were detected in the in vitro DNA binding features of POT1a and POT1b. In contrast to the repression of ATR signaling by POT1a, the ability of POT1b to control 5′-end resection was found to require two regions in the C terminus, one corresponding to the TPP1 binding domain and a second representing a new domain located between amino acids (aa) 300 and 350. Interestingly, the DNA binding domain of human POT1 can replace that of POT1a to repress ATR signaling, and the POT1b region from aa 300 to 350 required for the regulation of the telomere terminus is functionally conserved in human POT1. Thus, human POT1 combines the features of POT1a and POT1b.

scholarly journals Recognition of specific DNA sequences by the c-myb protooncogene product: role of three repeat units in the DNA-binding domain.

1993 ◽  
Vol 90 (20) ◽  
pp. 9320-9324 ◽  
Author(s):  
J. Tanikawa ◽  
T. Yasukawa ◽  
M. Enari ◽  
K. Ogata ◽  
Y. Nishimura ◽  
...  
Keyword(s):  
Dna Binding ◽  
Dna Sequences ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Repeat Units

scholarly journals Structure of the DNA-binding domain of human telomeric protein, TRF1 and its interaction with telomeric DNA

2001 ◽  
Vol 1 (1) ◽  
pp. 273-274 ◽  
Author(s):  
T. Nishikawa ◽  
H. Okamura ◽  
A. Nagadoi ◽  
P. Koig ◽  
D. Rhodes ◽  
...  
Keyword(s):  
Dna Binding ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Telomeric Dna ◽  
Telomeric Protein

scholarly journals An Engineered PAX3-KRAB Transcriptional Repressor Inhibits the Malignant Phenotype of Alveolar Rhabdomyosarcoma Cells Harboring the Endogenous PAX3-FKHR Oncogene

2000 ◽  
Vol 20 (14) ◽  
pp. 5019-5031 ◽  
Author(s):  
William J. Fredericks ◽  
Kasirajan Ayyanathan ◽  
Meenhard Herlyn ◽  
Josh R. Friedman ◽  
Frank J. Rauscher
Keyword(s):  
Dna Binding ◽  
Dna Sequences ◽  
Transcriptional Repression ◽  
Target Genes ◽  
Binding Domain ◽  
Stable Expression ◽  
Alveolar Rhabdomyosarcoma ◽  
Dna Binding Domain ◽  
Malignant Phenotype ◽  
Activation Domain

ABSTRACT The t(2;13) chromosomal translocation in alveolar rhabdomyosarcoma tumors (ARMS) creates an oncogenic transcriptional activator by fusion of PAX3 DNA binding motifs to a COOH-terminal activation domain derived from the FKHR gene. The dominant oncogenic potential of the PAX3-FKHR fusion protein is dependent on the FKHR activation domain. We have fused the KRAB repression module to the PAX3 DNA binding domain as a strategy to suppress the activity of the PAX3-FKHR oncogene. The PAX3-KRAB protein bound PAX3 target DNA sequences and repressed PAX3-dependent reporter plasmids. Stable expression of the PAX3-KRAB protein in ARMS cell lines resulted in loss of the ability of the cells to grow in low-serum or soft agar and to form tumors in SCID mice. Stable expression of a PAX3-KRAB mutant, which lacks repression function, or a KRAB protein alone, lacking a PAX3 DNA binding domain, failed to suppress the ARMS malignant phenotype. These data suggest that the PAX3-KRAB repressor functions as a DNA-binding-dependent suppressor of the transformed phenotype of ARMS cells, probably via competition with the endogenous PAX3-FKHR oncogene and repression of target genes required for ARMS tumorigenesis. The engineered repressor approach that directs a transcriptional repression domain to target genes deregulated by the PAX3-FKHR oncogene may be a useful strategy to identify the target genes critical for ARMS tumorigenesis.

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