scholarly journals A designed DNA binding motif that recognizes extended sites and spans two adjacent major grooves

2016 ◽  
Vol 7 (5) ◽  
pp. 3298-3303 ◽  
Author(s):  
Jéssica Rodríguez ◽  
Jesús Mosquera ◽  
Rebeca García-Fandiño ◽  
M. Eugenio Vázquez ◽  
José L. Mascareñas
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Rational Design ◽  
Binding Motif ◽  
Binding Peptide

We report the rational design of a DNA-binding peptide construct composed of the DNA-contacting regions of two transcription factors (GCN4 and GAGA) linked through an AT-hook DNA anchor.

scholarly journals The trihelix DNA-binding motif in higher plants is not restricted to the transcription factors GT-1 and GT-2

1998 ◽  
Vol 95 (6) ◽  
pp. 3318-3322 ◽  
Author(s):  
J. Smalle ◽  
J. Kurepa ◽  
M. Haegman ◽  
J. Gielen ◽  
M. Van Montagu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Higher Plants ◽  
Binding Motif

scholarly journals Structures of the activator ofK. pneumoniabiofilm formation, MrkH, indicates PilZ domains involved in c-di-GMP and DNA binding

2016 ◽  
Vol 113 (36) ◽  
pp. 10067-10072 ◽  
Author(s):  
Maria A. Schumacher ◽  
Wenjie Zeng
Keyword(s):  
Dna Binding ◽  
Rational Design ◽  
Domain Architecture ◽  
Klebsiella Pneumonia ◽  
Binding Motif ◽  
Genes Encoding ◽  
Biochemical Analyses ◽  
Biofilm Development ◽  
Domain Reorientation ◽  
Structure Stabilization

The pathogenesis ofKlebsiella pneumoniais linked to the bacteria’s ability to form biofilms. Mannose-resistantKlebsiella-like (Mrk) hemagglutinins are critical forK.pneumoniabiofilm development, and the expression of the genes encoding these proteins is activated by a 3′,5′-cyclic diguanylic acid (c-di-GMP)–regulated transcription factor, MrkH. To gain insight into MrkH function, we performed structural and biochemical analyses. Data revealed MrkH to be a monomer with a two-domain architecture consisting of a PilZ C-domain connected to an N domain that unexpectedly also harbors a PilZ-like fold. Comparison of apo- and c-di-GMP–bound MrkH structures reveals a large 138° interdomain rotation that is induced by binding an intercalated c-di-GMP dimer. c-di-GMP interacts with PilZ C-domain motifs 1 and 2 (RxxxR and D/NxSxxG) and a newly described c-di-GMP–binding motif in the MrkH N domain. Strikingly, these c-di-GMP–binding motifs also stabilize an open state conformation in apo MrkH via contacts from the PilZ motif 1 to residues in the C-domain motif 2 and the c-di-GMP–binding N-domain motif. Use of the same regions in apo structure stabilization and c-di-GMP interaction allows distinction between the states. Indeed, domain reorientation by c-di-GMP complexation with MrkH, which leads to a highly compacted structure, suggests a mechanism by which the protein is activated to bind DNA. To our knowledge, MrkH represents the first instance of specific DNA binding mediated by PilZ domains. The MrkH structures also pave the way for the rational design of inhibitors that targetK.pneumoniabiofilm formation.

scholarly journals Ubiquitin-Mediated Control of ETS Transcription Factors: Roles in Cancer and Development

2021 ◽  
Vol 22 (10) ◽  
pp. 5119
Author(s):  
Charles Ducker ◽  
Peter E. Shaw
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Expression Patterns ◽  
Malignant Cell ◽  
Mitogen Activated Protein Kinase ◽  
Cell Phenotype ◽  
Binding Motif ◽  
Ets Proteins ◽  
Protein Ubiquitination ◽  
Duplication Events

Genome expansion, whole genome and gene duplication events during metazoan evolution produced an extensive family of ETS genes whose members express transcription factors with a conserved winged helix-turn-helix DNA-binding domain. Unravelling their biological roles has proved challenging with functional redundancy manifest in overlapping expression patterns, a common consensus DNA-binding motif and responsiveness to mitogen-activated protein kinase signalling. Key determinants of the cellular repertoire of ETS proteins are their stability and turnover, controlled largely by the actions of selective E3 ubiquitin ligases and deubiquitinases. Here we discuss the known relationships between ETS proteins and enzymes that determine their ubiquitin status, their integration with other developmental signal transduction pathways and how suppression of ETS protein ubiquitination contributes to the malignant cell phenotype in multiple cancers.

DNA-binding specificities of the GATA transcription factor family

1993 ◽  
Vol 13 (7) ◽  
pp. 4011-4022
Author(s):  
L J Ko ◽  
J D Engel
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Target Genes ◽  
Polymerase Chain Reaction Amplification ◽  
Consensus Sequence ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Erythroid Cell ◽  
Binding Motif ◽  
Gata Factors

Members of the GATA family of transcription factors, which are related by a high degree of amino acid sequence identity within their zinc finger DNA-binding domains, each show distinct but overlapping patterns of tissue-restricted expression. Although GATA-1, -2, and -3 have been shown to recognize a consensus sequence derived from regulatory elements in erythroid cell-specific genes, WGATAR (in which W indicates A/T and R indicates A/G), the potential for more subtle differences in the binding preferences of each factor has not been previously addressed. By employing a binding selection and polymerase chain reaction amplification scheme with randomized oligonucleotides, we have determined the binding-site specificities of bacterially expressed chicken GATA-1, -2, and -3 transcription factors. Whereas all three GATA factors bind an AGATAA erythroid consensus motif with high affinity, a second, alternative consensus DNA sequence, AGATCTTA, is also recognized well by GATA-2 and GATA-3 but only poorly by GATA-1. These studies suggest that all three GATA factors are capable of mediating transcriptional effects via a common erythroid consensus DNA-binding motif. Furthermore, GATA-2 and GATA-3, because of their distinct expression patterns and broader DNA recognition properties, may be involved in additional regulatory processes beyond those of GATA-1. The definition of an alternative GATA-2-GATA-3 consensus sequence may facilitate the identification of new target genes in the further elucidation of the roles that these transcription factors play during development.

scholarly journals A Novel DNA-Binding Motif, Hallmark of a New Family of Plant Transcription Factors

2005 ◽  
Vol 137 (2) ◽  
pp. 602-606 ◽  
Author(s):  
José L. Carrasco ◽  
Gema Ancillo ◽  
María José Castelló ◽  
Pablo Vera
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Binding Motif ◽  
New Family

A Novel Zinc-binding Motif Revealed by Solution Structures of DNA-binding Domains of Arabidopsis SBP-family Transcription Factors

2004 ◽  
Vol 337 (1) ◽  
pp. 49-63 ◽  
Author(s):  
Kazuhiko Yamasaki ◽  
Takanori Kigawa ◽  
Makoto Inoue ◽  
Masaru Tateno ◽  
Tomoko Yamasaki ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Zinc Binding ◽  
Binding Motif ◽  
Solution Structures ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Zinc Binding Motif

scholarly journals Asm-1  +, a Neurospora crassa Gene Related to Transcriptional Regulators of Fungal Development

Genetics ◽  
1996 ◽  
Vol 144 (3) ◽  
pp. 991-1003 ◽  
Author(s):  
Rodolfo Aramayo ◽  
Yoav Peleg ◽  
Randolph Addison ◽  
Robert Metzenberg
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Transcription Factors ◽  
Dna Binding ◽  
Neurospora Crassa ◽  
Transcriptional Regulators ◽  
Protein Product ◽  
Binding Motif ◽  
Fungal Development ◽  
Male Specific ◽  
Related Proteins

Abstract This report describes the identification, cloning, and molecular analysis of Asm-1  + (Ascospore maturation 1), the Neurospora crassa homologue of the Aspergillus nidulans stuA (stunted A) gene. The Asm-1  + gene is constitutively transcribed and encodes an abundant, nucleus-localized 68.5-kD protein. The protein product of Asm-1  + (ASM-1), contains a potential DNA-binding motif present in related proteins from A. nidulans (StuA), Candida albicans (EFGTF-I), and Saccharomyces cerevisiae (Phd1 and Sok2). This motif is related to the DNA binding motif of the Swi4/Mbpl/Res family of transcription factors that control the cell cycle. Deletion of Asm-1  + destroys the ability to make protoperithecia (female organs), but does not affect male-specific functions. We propose that the APSES domain (ASM-1, Phdl, StuA, EFGTF-1, and Sok2) defines a group of proteins that constitute a family of related transcription factors involved in the control of fungal development.

scholarly journals DNA binding triggers tetramerization of the glucocorticoid receptor in live cells

2016 ◽  
Vol 113 (29) ◽  
pp. 8236-8241 ◽  
Author(s):  
Diego M. Presman ◽  
Sourav Ganguly ◽  
R. Louis Schiltz ◽  
Thomas A. Johnson ◽  
Tatiana S. Karpova ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Glucocorticoid Receptor ◽  
Rational Design ◽  
Quaternary Structure ◽  
Imaging Techniques ◽  
Steroid Receptor ◽  
Receptor Activation ◽  
Live Cells

Transcription factors dynamically bind to chromatin and are essential for the regulation of genes. Although a large percentage of these proteins appear to self-associate to form dimers or higher order oligomers, the stoichiometry of DNA-bound transcription factors has been poorly characterized in vivo. The glucocorticoid receptor (GR) is a ligand-regulated transcription factor widely believed to act as a dimer or a monomer. Using a unique set of imaging techniques coupled with a cell line containing an array of DNA binding elements, we show that GR is predominantly a tetramer when bound to its target DNA. We find that DNA binding triggers an interdomain allosteric regulation within the GR, leading to tetramerization. We therefore propose that dynamic changes in GR stoichiometry represent a previously unidentified level of regulation in steroid receptor activation. Quaternary structure analysis of other members of the steroid receptor family (estrogen, androgen, and progesterone receptors) reveals variation in oligomerization states among this family of transcription factors. Because GR’s oligomerization state has been implicated in therapy outcome, our findings open new doors to the rational design of novel GR ligands and redefine the quaternary structure of steroid receptors.

scholarly journals DNA-binding specificities of the GATA transcription factor family.

1993 ◽  
Vol 13 (7) ◽  
pp. 4011-4022 ◽  
Author(s):  
L J Ko ◽  
J D Engel
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Target Genes ◽  
Polymerase Chain Reaction Amplification ◽  
Consensus Sequence ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Erythroid Cell ◽  
Binding Motif ◽  
Gata Factors

Members of the GATA family of transcription factors, which are related by a high degree of amino acid sequence identity within their zinc finger DNA-binding domains, each show distinct but overlapping patterns of tissue-restricted expression. Although GATA-1, -2, and -3 have been shown to recognize a consensus sequence derived from regulatory elements in erythroid cell-specific genes, WGATAR (in which W indicates A/T and R indicates A/G), the potential for more subtle differences in the binding preferences of each factor has not been previously addressed. By employing a binding selection and polymerase chain reaction amplification scheme with randomized oligonucleotides, we have determined the binding-site specificities of bacterially expressed chicken GATA-1, -2, and -3 transcription factors. Whereas all three GATA factors bind an AGATAA erythroid consensus motif with high affinity, a second, alternative consensus DNA sequence, AGATCTTA, is also recognized well by GATA-2 and GATA-3 but only poorly by GATA-1. These studies suggest that all three GATA factors are capable of mediating transcriptional effects via a common erythroid consensus DNA-binding motif. Furthermore, GATA-2 and GATA-3, because of their distinct expression patterns and broader DNA recognition properties, may be involved in additional regulatory processes beyond those of GATA-1. The definition of an alternative GATA-2-GATA-3 consensus sequence may facilitate the identification of new target genes in the further elucidation of the roles that these transcription factors play during development.

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