Sequential assignments of the proton NMR resonances of zinc(II)2 and cadmium-113(II)2 derivatives of the DNA-binding domain of the GAL4 transcription factor reveal a novel structural motif for specific DNA recognition

Biochemistry ◽  
1991 ◽  
Vol 30 (17) ◽  
pp. 4212-4222 ◽  
Author(s):  
Tao Pan ◽  
Joseph E. Coleman
Keyword(s):  
Transcription Factor ◽  
Dna Binding ◽  
Dna Recognition ◽  
Proton Nmr ◽  
Binding Domain ◽  
Structural Motif ◽  
Dna Binding Domain ◽  
Derivatives Of

NMR Structure of Transcription Factor Sp1 DNA Binding Domain†,‡

Biochemistry ◽  
2004 ◽  
Vol 43 (51) ◽  
pp. 16027-16035 ◽  
Author(s):  
Shinichiro Oka ◽  
Yasuhisa Shiraishi ◽  
Takuya Yoshida ◽  
Tadayasu Ohkubo ◽  
Yukio Sugiura ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Dna Binding ◽  
Binding Domain ◽  
Nmr Structure ◽  
Dna Binding Domain ◽  
Transcription Factor Sp1

scholarly journals Solution Structure of the DNA-Binding Domain of the Tomato Heat-Stress Transcription Factor HSF24

1996 ◽  
Vol 236 (3) ◽  
pp. 911-921 ◽  
Author(s):  
Jurgen Schultheiss ◽  
Olaf Kunert ◽  
Uwe Gase ◽  
Klaus-Dieter Scharf ◽  
Lutz Nover ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Heat Stress ◽  
Dna Binding ◽  
Solution Structure ◽  
Binding Domain ◽  
Dna Binding Domain

scholarly journals Adaptive evolution of transcription factor binding affinities

2017 ◽  
Author(s):  
Jungeui Hong ◽  
Nathan Brandt ◽  
Ally Yang ◽  
Tim Hughes ◽  
David Gresham
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Dna Binding ◽  
Adaptive Evolution ◽  
Consensus Sequence ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Missense Mutations ◽  
Binding Affinities ◽  
Synonymous Mutations

Understanding the molecular basis of gene expression evolution is a central problem in evolutionary biology. However, connecting changes in gene expression to increased fitness, and identifying the functional basis of those changes, remains challenging. To study adaptive evolution of gene expression in real time, we performed long term experimental evolution (LTEE) of Saccharomyces cerevisiae (budding yeast) in ammonium-limited chemostats. Following several hundred generations of continuous selection we found significant divergence of nitrogen-responsive gene expression in lineages with increased fitness. In multiple independent lineages we found repeated selection for non-synonymous mutations in the zinc finger DNA binding domain of the activating transcription factor (TF), GAT1, that operates within incoherent feedforward loops to control expression of the nitrogen catabolite repression (NCR) regulon. Missense mutations in the DNA binding domain of GAT1 reduce its binding affinity for the GATAA consensus sequence in a promoter-specific manner, resulting in increased expression of ammonium permease genes via both direct and indirect effects, thereby conferring increased fitness. We find that altered transcriptional output of the NCR regulon results in antagonistic pleiotropy in alternate environments and that the DNA binding domain of GAT1 is subject to purifying selection in natural populations. Our study shows that adaptive evolution of gene expression can entail tuning expression output by quantitative changes in TF binding affinities while maintaining the overall topology of a gene regulatory network.

Structure, function, and dynamics of the dimerization and DNA-binding domain of oncogenic transcription factor v-Myc11Edited by P. E. Wright

2001 ◽  
Vol 307 (5) ◽  
pp. 1395-1410 ◽  
Author(s):  
Wolfgang Fieber ◽  
Martin L. Schneider ◽  
Theresia Matt ◽  
Bernhard Kräutler ◽  
Robert Konrat ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Dna Binding ◽  
Structure Function ◽  
Binding Domain ◽  
Factor V ◽  
Dna Binding Domain ◽  
Oncogenic Transcription Factor

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 Activation of a Development-Specific Gene, dofA, by FruA, an Essential Transcription Factor for Development of Myxococcus xanthus

2005 ◽  
Vol 187 (24) ◽  
pp. 8504-8506 ◽  
Author(s):  
Toshiyuki Ueki ◽  
Sumiko Inouye
Keyword(s):  
Transcription Factor ◽  
Dna Binding ◽  
Myxococcus Xanthus ◽  
Binding Domain ◽  
Specific Gene ◽  
Dna Binding Domain ◽  
Gel Shift ◽  
Essential Transcription Factor

ABSTRACT FruA is an essential transcription factor for Myxococcus xanthus development. The expression of tps and dofA genes is fruA dependent. In this study, we show by gel shift and footprint assays with the C-terminal DNA-binding domain of FruA and by a lacZ fusion assay that FruA may directly activate dofA expression during development.

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