DNA-Binding Specificity of Mutant Glucocorticoid Receptor DNA-Binding Domains

1993 ◽  
Vol 684 (1 Zinc-Finger P) ◽  
pp. 253-256 ◽  
Author(s):  
JOHANNA ZILLIACUS ◽  
ANTHONY P. H. WRIGHT ◽  
ULF NORINDER ◽  
JAN-ÅKE GUSTAFSSON
Keyword(s):  
Dna Binding ◽  
Glucocorticoid Receptor ◽  
Binding Specificity ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Dna Binding Specificity

scholarly journals DNA binding specificity of mutant glucocorticoid receptor DNA-binding domains.

1991 ◽  
Vol 266 (5) ◽  
pp. 3101-3106
Author(s):  
J Zilliacus ◽  
K Dahlman-Wright ◽  
A Wright ◽  
J A Gustafsson ◽  
J Carlstedt-Duke
Keyword(s):  
Dna Binding ◽  
Glucocorticoid Receptor ◽  
Binding Specificity ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Dna Binding Specificity

scholarly journals On exploring effects of coevolving residues on DNA binding specificity of transcription factors

2021 ◽  
Author(s):  
Yizhao Luan ◽  
Zhi Xie
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Binding Specificity ◽  
Binding Activity ◽  
Dna Interactions ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Dna Binding Activity ◽  
Dna Binding Specificity ◽  
The Stability

Transcription factors (TFs) regulate gene expression by specifically binding to DNA targets. Many factors have been revealed to influence TF-DNA binding specificity. Coevolution of residues in proteins occurs due to a common evolutionary history. However, it is unclear how coevolving residues in TFs contribute to DNA binding specificity. Here, we systematically analyzed TF-DNA interactions from high-throughput experiments for seven TF families, including Homeobox, HLH, bZIP_1, Ets, HMG_box, zf-C4 and Zn_clus TFs. Based on TF-DNA interactions, we detected TF subclass determining sites (TSDSs) defining the heterogeneity of DNA binding preference for each TF family. We showed that the TSDSs were more likely to be coevolving with TSDSs than with non-TSDSs, particularly for Homeobox, HLH, Ets, bZIP_1 and HMG_box TF families. Mutation of the highly coevolving residues could significantly reduce the stability of TF-DNA complex. The distant residues from the DNA interface also contributed to TF-DNA binding activity. Overall, our study gave evidence of the functional importance of coevolved residues in refining transcriptional regulation and provided clues to the application of engineered DNA-binding domains and protein.

scholarly journals DNA-binding specificity of GATA family transcription factors.

1993 ◽  
Vol 13 (7) ◽  
pp. 3999-4010 ◽  
Author(s):  
M Merika ◽  
S H Orkin
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Mammalian Cells ◽  
Chimeric Protein ◽  
Binding Specificity ◽  
Mobility Shift ◽  
Binding Domains ◽  
Dna Binding Specificity ◽  
Mobility Shift Assay ◽  
Gata Family

GATA-binding proteins constitute a family of transcription factors that recognize a target site conforming to the consensus WGATAR (W = A or T and R = A or G). Here we have used the method of polymerase chain reaction-mediated random site selection to assess in an unbiased manner the DNA-binding specificity of GATA proteins. Contrary to our expectations, we show that GATA proteins bind a variety of motifs that deviate from the previously assigned consensus. Many of the nonconsensus sequences bind protein with high affinity, equivalent to that of conventional GATA motifs. By using the selected sequences as probes in the electrophoretic mobility shift assay, we demonstrate overlapping, but distinct, sequence preferences for GATA family members, specified by their respective DNA-binding domains. Furthermore, we provide additional evidence for interaction of amino and carboxy fingers of GATA-1 in defining its binding site. By performing cotransfection experiments, we also show that transactivation parallels DNA binding. A chimeric protein containing the finger domain of areA and the activation domains of GATA-1 is capable of activating transcription in mammalian cells through GATA motifs. Our findings suggest a mechanism by which GATA proteins might selectively regulate gene expression in cells in which they are coexpressed.

N-terminal DNA-binding domains contribute to differential DNA-binding specificities of NF-kappa B p50 and p65

1993 ◽  
Vol 13 (2) ◽  
pp. 852-860
Author(s):  
M B Toledano ◽  
D Ghosh ◽  
F Trinh ◽  
W J Leonard
Keyword(s):  
Dna Binding ◽  
Point Mutations ◽  
Terminal Region ◽  
Sequence Motif ◽  
Structural Determinants ◽  
Nf Kappa B ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Dna Binding Specificity

We previously reported that either oxidation or alkylation of NF-kappa B in vitro abrogates DNA binding. We used this phenomenon to help elucidate structural determinants of NF-kappa B binding. We now demonstrate that Cys-62 of NF-kappa B p50 mediates the redox effect and lies within an N-terminal region required for DNA binding but not for dimerization. Several point mutations in this region confer a transdominant negative binding phenotype to p50. The region is highly conserved in all Rel family proteins, and we have determined that it is also critical for DNA binding of NF-kappa B p65. Replacement of the N-terminal region of p65 with the corresponding region from p50 changes its DNA-binding specificity towards that of p50. These data suggest that the N-terminal regions of p50 and p65 are critical for DNA binding and help determine the DNA-binding specificities of p50 and p65. We have defined within the N-terminal region a sequence motif, R(F/G)(R/K)YXCE, which is present in Rel family proteins and also in zinc finger proteins capable of binding to kappa B sites. The potential significance of this finding is discussed.

Nuclear Extracts Enhance Gel Retardation with Androgen and Glucocorticoid Receptor DNA-Binding Domains

1993 ◽  
Vol 684 (1 Zinc-Finger P) ◽  
pp. 202-204 ◽  
Author(s):  
PIET VOS ◽  
FRANK CLAESSENS ◽  
LINDA CELIS ◽  
WALTER HEYNS ◽  
WILFRIED ROMBAUTS ◽  
...  
Keyword(s):  
Dna Binding ◽  
Glucocorticoid Receptor ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Gel Retardation ◽  
Nuclear Extracts

scholarly journals DNA-binding specificity of NGFI-A and related zinc finger transcription factors.

1995 ◽  
Vol 15 (4) ◽  
pp. 2275-2287 ◽  
Author(s):  
A H Swirnoff ◽  
J Milbrandt
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Target Genes ◽  
Zinc Fingers ◽  
Consensus Sequence ◽  
Binding Specificity ◽  
Early Gene ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Random Site

NGFI-A is the prototypic member of a family of immediate-early gene-encoded transcription factors which includes NGFI-C, Egr3, and Krox20. These proteins possess highly homologous DNA-binding domains, composed of three Cys2-His2 zinc fingers, and all bind to and activate transcription from the sequence GCGGGGGCG. We used a PCR-mediated random site selection protocol to determine whether other sites could be bound by these proteins and the extent to which their binding site preferences are similar or different. The high-affinity consensus sites generated from the selection data are similar, and the combined consensus sequence is T-G-C-G-T/g-G/A-G-G-C/a/t-G-G/T (lowercase letters indicate bases selected less frequently). Using gel shift assays, we found that sequences that diverge from the consensus were bound by NGFI-A, confirming that there is greater variability in binding sites than has generally been acknowledged. We also provide evidence that protein-DNA interactions not noted, or whose importance was not apparent from the X-ray cocrystal structure of the NGFI-A zinc fingers complexed with DNA, contribute significantly to the binding energy of these proteins and confirm that an optimal site is at least 10 instead of 9 nucleotides in length. In contrast to the similarities in binding specificity among these proteins we found that while NGFI-A, Egr3, and Krox20 have comparable DNA binding affinities and kinetics of dissociation, the affinity of NGFI-C is more than threefold lower. This could result in differential regulation of target genes in cells where NGFI-C and the other proteins are coexpressed. Furthermore, we show that this affinity difference is a property not of the zinc fingers themselves but rather of the protein context of the DNA-binding domain.

Reaction of tyrosyl-modifying reagents with the ligand- and DNA-binding domains of the rabbit liver glucocorticoid receptor

1990 ◽  
Vol 36 (1-2) ◽  
pp. 15-23 ◽  
Author(s):  
Philippe Blanchardie ◽  
Marc Denis ◽  
Jean-Luc Orsonneau ◽  
Patrick Lustenberger
Keyword(s):  
Dna Binding ◽  
Glucocorticoid Receptor ◽  
Rabbit Liver ◽  
Dna Binding Domains ◽  
Binding Domains

scholarly journals Transcriptional re-wiring by mutation of the yeast Hsf1 oligomerization domain

2020 ◽  
Author(s):  
Elizabeth A. Morton ◽  
Michael W. Dorrity ◽  
Wei Zhou ◽  
Stanley Fields ◽  
Christine Queitsch
Keyword(s):  
Heat Stress ◽  
Dna Binding ◽  
Sequence Variation ◽  
Heat Shock Transcription Factors ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Dna Binding Specificity ◽  
Evolutionarily Conserved ◽  
Oligomerization Domain

AbstractResponse to heat stress is mediated by heat shock transcription factors (HSFs), which possess conserved DNA-binding and oligomerization domains. The oligomerization domain is required for HSF1 to transition under heat stress from a monomer to a homotrimer, which alters DNA-binding specificity and affinity. Sequence variation in the oligomerization domain affects HSF1 activity, although this link is poorly understood. We performed a deep mutational scan of >400,000 variants of the oligomerization domain of Saccharomyces cerevisiae Hsf1 and measured fitness under stress and non-stress conditions. We identify mutations that confer temperature-specific phenotypes; some exceptional Hsf1variants lead to enhanced growth under heat stress and changes to in vivo DNA-binding and transcriptional programs. The link between Hsf1 oligomerization and DNA-binding domain is evolutionarily conserved, with co-evolving residues between these domains found among fungi. Mutation of transcription factor oligomerization domains may represent a path toward re-wiring transcriptional programs without mutation of DNA-binding domains.

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