scholarly journals Structure of WT1 zinc fingers bound to its cognate DNA: Implications of the KTS insert

2018 ◽  
Author(s):  
Raymond K. Yengo ◽  
Elmar Nurmemmedov ◽  
Marjolein M.G.M. Thunnissen
Keyword(s):  
Crystal Structure ◽  
Transcription Factor ◽  
Amino Acid ◽  
Dna Binding ◽  
Rna Splicing ◽  
Zinc Fingers ◽  
Dna Recognition ◽  
Life Forms ◽  
Target Dna ◽  
Partner Proteins

ABSTRACTWT1 is a transcription factor with a DNA binding N-terminal domain containing four C2H2-type zinc fingers. In order to perform its role as a transcription factor, WT1 needs to specifically recognize and properly bind to its target DNA. How this is done is still not completely clear. Two of WT1’s major isoforms are distinguished by the presence or absence of a 3 amino acid insert, Lysine-Threonine-Serine (KTS) in the linker between zinc-fingers 3 and 4. This KTS insert is conserved throughout all life forms expressing WT1. The –KTS isoform, which acts as a transcription factor, binds DNA with higher affinity than the +KTS isoform, which is thought to participate in RNA splicing and interaction with partner proteins. This study was aims at elucidating the effect of the KTS insert on DNA binding. Here we present the crystal structure of WT1 zinc fingers 2-4, with and without the KTS insert, bound to the WT1 9-base pair cognate DNA sequence, refined to 1.9 Å and 2.5 Å respectively. The structures show that the +KTS isoform of WT1 recognizes DNA with the same specificity as the –KTS isoform. The only differences in the DNA bound conformation of the two isoforms are found within the linker containing the KTS, and these mainly involve the loss of the C-capping interactions thought to stabilize the complex. These structures provide the molecular detail necessary for the interpretation of the WT1 transcriptional DNA recognition and validation of its transcriptional targets.

scholarly journals Evolutionary Analysis of Transcriptional Regulation Mediated by Cdx2 in Rodents

2021 ◽  
Author(s):  
Weizheng Liang ◽  
Guipeng Li ◽  
Huanhuan Cui ◽  
Yukai Wang ◽  
Wencheng Wei ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Amino Acid ◽  
Dna Binding ◽  
Phenotypic Diversity ◽  
Embryonic Stem ◽  
Regulatory Elements ◽  
Evolutionary Analysis ◽  
Protein Sequence Analysis ◽  
Systematic Analysis

AbstractDifferences in gene expression, which can arise from divergence in cis-regulatory elements or alterations in transcription factors binding specificity, are one of the most important causes of phenotypic diversity during evolution. By protein sequence analysis, we observed high sequence conservation in the DNA binding domain (DBD) of the transcription factor Cdx2 across many vertebrates, whereas three amino acid changes were exclusively found in mouse Cdx2 (mCdx2), suggesting potential positive selection in the mouse lineage. Multi-omics analyses were then carried out to investigate the effects of these changes. Surprisingly, there were no significant functional differences between mCdx2 and its rat homologue (rCdx2), and none of the three amino acid changes had any impact on its function. Finally, we used rat-mouse allodiploid embryonic stem cells (RMES) to study the cis effects of Cdx2-mediated gene regulation between the two rodents. Interestingly, whereas Cdx2 binding is largely divergent between mouse and rat, the transcriptional effect induced by Cdx2 is conserved to a much larger extent.Author summaryOur study 1) represented a first systematic analysis of species-specific adaptation in DNA binding pattern of transcription factor. Although the mouse-specific amino acid changes did not manifest functional impact in our system, several explanations may account for it (See Discussion part for the detail); 2) represented a first study of cis-regulation between two reproductively isolated species by using a novel allodiploid system; 3) demonstrated a higher conservation of transcriptional output than that of DNA binding, suggesting the evolvability/plasticity of the latter; 4) finally provided a rich data resource for Cdx2 mediated regulation, including gene expression, chromatin accessibility and DNA binding etc.

Transcriptional activity of the zinc finger protein NGFI-A is influenced by its interaction with a cellular factor

1993 ◽  
Vol 13 (11) ◽  
pp. 6858-6865
Author(s):  
M W Russo ◽  
C Matheny ◽  
J Milbrandt
Keyword(s):  
Transcription Factor ◽  
Dna Binding ◽  
Transcriptional Activity ◽  
Zinc Fingers ◽  
Fold Increase ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Activation Domains ◽  
Cellular Factor ◽  
Inhibitory Domain

NGFI-A is an immediate-early gene that encodes a transcription factor whose DNA-binding domain is composed of three zinc fingers. To define the domains responsible for its transcriptional activity, a mutational analysis was conducted with an NGFI-A molecule in which the zinc fingers were replaced by the GAL4 DNA-binding domain. In a cotransfection assay, four activation domains were found within NGFI-A. Three of the activation domains are similar to those characterized previously: one contains a large number of acidic residues, another is enriched in proline and glutamine residues, and another has some sequence homology to a domain found in Krox-20. The fourth bears no resemblance to previously described activation domains. NGFI-A also contains an inhibitory domain whose removal resulted in a 15-fold increase in NGFI-A activity. This increase in activity occurred in all mammalian cell types tested but not in Drosophila S2 cells. Competition experiments in which increasing amounts of the inhibitory domain were cotransfected along with NGFI-A demonstrated a dose-dependent increase in NGFI-A activity. A point mutation within the inhibitory domain of the competitor (I293F) abolished this property. When the analogous mutation was introduced into native NGFI-A, a 17-fold increase in activity was observed. The inhibitory effect therefore appears to be the result of an interaction between this domain and a titratable cellular factor which is weakened by this mutation. Downmodulation of transcription factor activity through interaction with a cellular factor has been observed in several other systems, including the regulation of transcription factor E2F by retinoblastoma protein, and in studies of c-Jun.

scholarly journals Two monomers of yeast transcription factor ADR1 bind a palindromic sequence symmetrically to activate ADH2 expression.

1991 ◽  
Vol 11 (3) ◽  
pp. 1566-1577 ◽  
Author(s):  
S K Thukral ◽  
A Eisen ◽  
E T Young
Keyword(s):  
Transcription Factor ◽  
Amino Acid ◽  
Dna Binding ◽  
Dimethyl Sulfate ◽  
Binding Activity ◽  
Single Amino Acid ◽  
Minor Effect ◽  
Palindromic Sequence ◽  
Amino Terminal ◽  
Dna Binding Activity

ADR1 is a transcription factor from Saccharomyces cerevisiae that regulates ADH2 expression through a 22-bp palindromic sequence (UAS1). Size fractionation studies revealed that full-length ADR1 and a truncated ADR1 protein containing the first 229 amino acids, which has the complete DNA-binding domain, ADR1:17-229, exist as monomers in solution. However, two complexes were formed with target DNA-binding sites. UV-cross-linking studies suggested that these two complexes represent one and two molecules of ADR1 bound to DNA. Studies of ADR1 complexes formed with wild-type UAS1, asymmetrically altered UAS1, and one half of UAS1 showed that ADR1 can bind to one half of UAS1 and gives rise to a complex containing one molecule of ADR1. Dimethyl sulfate interference studies were consistent with this interpretation and in addition indicated that purine contact sites in each half of UAS1 were identical. Increasing the distance between the two halves of UAS1 had at most a minor effect of the thermodynamics of formation of the two complexes. These data are more consistent with ADR1 binding as two independent monomers, one to each half of UAS1. However, binding of two ADR1 monomers at UAS1 is apparently essential for transactivation in vivo. Further, we have identified a stretch of 18 amino acid residues amino terminal to the zinc two-finger domains of ADR1 which is essential for DNA-binding activity. Single amino acid substitutions of residues in this region resulted in severely reduced DNA-binding activity.

scholarly journals Filamin A-Bound PEBP2β/CBFβ Is Retained in the Cytoplasm and Prevented from Functioning as a Partner of the Runx1 Transcription Factor

2005 ◽  
Vol 25 (3) ◽  
pp. 1003-1012 ◽  
Author(s):  
Naomi Yoshida ◽  
Takehiro Ogata ◽  
Kenji Tanabe ◽  
Songhua Li ◽  
Megumi Nakazato ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Amino Acid ◽  
Dna Binding ◽  
Binding Domain ◽  
Actin Binding ◽  
Regulatory Domain ◽  
Amino Acid Residues ◽  
Filamin A ◽  
Actin Binding Protein ◽  
Binding Subunit

ABSTRACT The heterodimeric transcription factor PEBP2/CBF is composed of a DNA-binding subunit, called Runx1, and a non-DNA-binding subunit, called PEBP2β/CBFβ. The Runx1 protein is detected exclusively in the nuclei of most cells and tissues, whereas PEBP2β is located in the cytoplasm. We addressed the mechanism by which PEBP2β localizes to the cytoplasm and found that it is associated with filamin A, an actin-binding protein. Filamin A retains PEBP2β in the cytoplasm, thereby hindering its engagement as a Runx1 partner. The interaction with filamin A is mediated by a region within PEBP2β that includes amino acid residues 68 to 93. The deletion of this region or the repression of filamin A enables PEBP2β to translocate to the nucleus. Based on these observations, we propose that PEBP2β has two distinct domains, a newly defined regulatory domain that interacts with filamin A and the previously identified Runx1-binding domain.

Identification of amino acid residues of transcription factor AP-2 involved in DNA binding 1 1Edited by M. Yaniv

2000 ◽  
Vol 301 (4) ◽  
pp. 807-816 ◽  
Author(s):  
Miguel Angel Garcı́a ◽  
Mónica Campillos ◽  
Samuel Ogueta ◽  
Fernando Valdivieso ◽  
Jesús Vázquez
Keyword(s):  
Transcription Factor ◽  
Amino Acid ◽  
Dna Binding ◽  
Amino Acid Residues

Relative Contributions of the Zinc Fingers of Transcription Factor IIIA to the Energetics of DNA Binding

1994 ◽  
Vol 244 (1) ◽  
pp. 23-25 ◽  
Author(s):  
Karen R. Clemens ◽  
Penghua Zhang ◽  
Xiubei Liao ◽  
Steven J. McBryant ◽  
Peter E. Wright ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Dna Binding ◽  
Zinc Fingers ◽  
Transcription Factor Iiia

scholarly journals Balance between mutually exclusive traits shifted by variants of a yeast transcription factor

2017 ◽  
Author(s):  
Michael W. Dorrity ◽  
Josh T. Cuperus ◽  
Jolie A. Carlisle ◽  
Stanley Fields ◽  
Christine Queitsch
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Transcription Factor ◽  
Amino Acid ◽  
Dna Binding ◽  
Single Amino Acid ◽  
Environmental Cues ◽  
Dna Binding Domain ◽  
Independent Manner ◽  
Half Site

AbstractIn Saccharomyces cerevisiae, the decision to mate or invade relies on environmental cues that converge on a shared transcription factor, Ste12. Specificity toward invasion occurs via Ste12 binding cooperatively with the co-factor Tec1. Here, we characterize the in vitro binding preferences of Ste12 to identify a defined spacing and orientation of dimeric sites, one that is common in pheromone-regulated genes. We find that single amino acid changes in the DNA-binding domain of Ste12 can shift the preference of yeast toward either mating or invasion. These mutations define two distinct regions of this domain, suggesting alternative modes of DNA binding for each trait. Some exceptional Ste12 mutants promote hyperinvasion in a Tec1-independent manner; these fail to bind cooperative sites with Tec1 and bind to unusual dimeric Ste12 sites that contain one highly degenerate half site. We propose a model for how activation of invasion genes could have evolved with Ste12 alone.

scholarly journals Functional and conserved domains of the Drosophila transcription factor encoded by the segmentation gene knirps

1994 ◽  
Vol 14 (12) ◽  
pp. 7899-7908
Author(s):  
N Gerwin ◽  
A La Rosée ◽  
F Sauer ◽  
H P Halbritter ◽  
M Neumann ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Amino Acid ◽  
Dna Binding ◽  
Broad Band ◽  
Binding Domain ◽  
Orphan Receptor ◽  
Dna Binding Domain ◽  
Coding Region ◽  
Amino Acid Region

The Drosophila gap gene knirps (kni) is required for abdominal segmentation. It encodes a steroid/thyroid orphan receptor-type transcription factor which is distributed in a broad band of nuclei in the posterior region of the blastoderm. To identify essential domains of the kni protein (KNI), we cloned and sequenced the DNA encompassing the coding region of nine kni mutant alleles of different strength and kni-homologous genes of related insect species. We also examined in vitro-modified versions of KNI in various assay systems both in vitro and in tissue culture. The results show that KNI contains several functional domains which are arranged in a modular fashion. The N-terminal 185-amino-acid region which includes the DNA-binding domain and a functional nuclear location signal fails to provide kni activity to the embryo. However, a truncated KNI protein that contains additional 47 amino acids exerts rather strong kni activity which is functionally defined by a weak kni mutant phenotype of the embryo. The additional 47-amino-acid stretch includes a transcriptional repressor domain which acts in the context of a heterologous DNA-binding domain of the yeast transcriptional activator GAL4. The different domains of KNI as defined by functional studies are conserved during insect evolution.

Crystal Structure and DNA Binding of the Homeodomain of the Stem Cell Transcription Factor Nanog

2008 ◽  
Vol 376 (3) ◽  
pp. 758-770 ◽  
Author(s):  
Ralf Jauch ◽  
Calista Keow Leng Ng ◽  
Kumar Singh Saikatendu ◽  
Raymond C. Stevens ◽  
Prasanna R. Kolatkar
Keyword(s):  
Crystal Structure ◽  
Transcription Factor ◽  
Stem Cell ◽  
Dna Binding
Sign in / Sign up

Export Citation Format

Share Document