The DNA-binding domain of the yeast Saccharomyces cerevisiae CYP1(HAP1) transcription factor possesses two zinc ions which are complexed in a zinc cluster

1994 ◽  
Vol 225 (2) ◽  
pp. 593-599 ◽  
Author(s):  
Johanna E. Timmerman ◽  
Bernard Guiard ◽  
Evelyne Shechter ◽  
Marc-Andre Delsuc ◽  
Jean-Yves Lallemand ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Transcription Factor ◽  
Dna Binding ◽  
Binding Domain ◽  
Zinc Ions ◽  
Dna Binding Domain ◽  
Yeast Saccharomyces Cerevisiae ◽  
Zinc Cluster

scholarly journals Properties of the DNA-binding domain of the Saccharomyces cerevisiae STE12 protein.

1991 ◽  
Vol 11 (12) ◽  
pp. 5910-5918 ◽  
Author(s):  
Y L Yuan ◽  
S Fields
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Amino Acids ◽  
Dna Binding ◽  
Binding Affinity ◽  
Binding Domain ◽  
Upstream Region ◽  
Dna Binding Domain ◽  
Yeast Saccharomyces Cerevisiae ◽  
Dnase I Footprinting

The STE12 protein of the yeast Saccharomyces cerevisiae binds to the pheromone response element (PRE) present in the upstream region of genes whose transcription is induced by pheromone. Using DNase I footprinting assays with bacterially made STE12 fragments, we localized the DNA-binding domain to 164 amino acids near the amino terminus. Footprinting of oligonucleotide-derived sequences containing one PRE, or two PREs in head-to-tail or tail-to-tail orientation, showed that the N-terminal 215 amino acids of STE12 has similar binding affinity to either of the dimer sites and a binding affinity 5- to 10-fold lower for the monomer site. This binding cooperativity was also evident on a fragment from the MFA2 gene, which encodes the a-factor pheromone. On this fragment, the 215-amino-acid STE12 fragment protected both a consensus PRE as well as a degenerate PRE containing an additional residue. Mutation of the degenerate site led to a 5- to 10-fold decrease in binding; mutation of the consensus site led to a 25-fold decrease in binding. The ability of PREs to function as pheromone-inducible upstream activation sequences in yeast correlated with their ability to bind the STE12 domain in vitro. The sequence of the STE12 DNA-binding domain contains similarities to the homeodomain, although it is highly diverged from other known examples of this motif. Moreover, the alignment between STE12 and the homeodomain postulates loops after both the putative helix 1 and helix 2 of the STE12 sequence.

scholarly journals The Saccharomyces cerevisiae MADS-box transcription factor Rlm1 is a target for the Mpk1 mitogen-activated protein kinase pathway.

1997 ◽  
Vol 17 (4) ◽  
pp. 1848-1859 ◽  
Author(s):  
E Dodou ◽  
R Treisman
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Transcription Factor ◽  
Dna Binding ◽  
Transcriptional Activation ◽  
Mapk Pathway ◽  
Consensus Sequence ◽  
Binding Domain ◽  
Mitogen Activated Protein Kinase ◽  
Dna Binding Domain ◽  
Mads Box

Mutation of Saccharomyces cerevisiae RLM1, which encodes a MADS-box transcription factor, confers resistance to the toxic effects of constitutive activity of the Mpk1 mitogen-activated kinase (MAPK) pathway. The Rlm1 DNA-binding domain, which is similar to that of the metazoan MEF2 transcription factors, is also closely related to that of a second S. cerevisiae protein, Smp1 (second MEF2-like protein), encoded by the YBR182C open reading frame (N. Demolis et al., Yeast 10:1511-1525, 1994; H. Feldmann et al., EMBO J. 13:5795-5809, 1994). We show that Rlm1 and Smp1 have MEF2-related DNA-binding specificities: Rlm1 binds with the same specificity as MEF2, CTA(T/A)4TAG, while SMP1 binds a more extended consensus sequence, ACTACTA(T/A)4TAG. The two DNA-binding domains can heterodimerize with each other and with MEF2A. Deletion of RLM1 enhances resistance to cell wall disruptants, increases saturation density, reduces flocculation, and inactivates reporter genes controlled by the Rlm1 consensus binding site. Deletion of SMP1 neither causes these phenotypes nor enhances the Rlm1 deletion phenotype. However, overexpression of the DNA-binding domain of either protein causes an osmoremedial phenotype. Synthetic and naturally occurring MEF2 consensus sequences exhibit strong RLM1- and MPK1-dependent upstream activation sequence activity. Transcriptional activation by Rlm1 requires its C-terminal sequences, and Gal4 fusion proteins containing Rlm1 C-terminal sequences also act as MPK1-dependent transcriptional activators. These results establish the Rlm1 C-terminal sequences as a target for the Mpk1 MAPK pathway.

scholarly journals The DNA-binding domain of CaNdt80p is required to activate CDR1 involved in drug resistance in Candida albicans

2006 ◽  
Vol 55 (10) ◽  
pp. 1403-1411 ◽  
Author(s):  
Jang-Shiun Wang ◽  
Yun-Liang Yang ◽  
Chin-Jung Wu ◽  
Karen J. Ouyang ◽  
Kuo-Yun Tseng ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Drug Resistance ◽  
Transcription Factor ◽  
Candida Albicans ◽  
Dna Binding ◽  
Efflux Pump ◽  
Binding Domain ◽  
Null Mutation ◽  
Dna Binding Domain ◽  
Positive Regulator

CaNdt80p, the Candida albicans homologue of the Saccharomyces cerevisiae transcription factor ScNdt80p, has been identified as a positive regulator of CDR1, which encodes an efflux pump involved in drug resistance in C. albicans. To investigate the involvement of the putative DNA-binding domain of CaNdt80p in drug resistance, chimeras of CaNdt80p and ScNdt80p were constructed. Interestingly, the DNA-binding domain of ScNdt80p could functionally complement that of CaNdt80p to activate CDR1p–lacZ in S. cerevisiae. Consistently, CaNdt80p containing a mutation in the DNA-binding domain failed to activate CDR1p–lacZ in S. cerevisiae. Furthermore, a copy of CaNDT80 with the same mutation also failed to complement the drug-sensitive phenotype caused by a null mutation in C. albicans. Thus, the DNA-binding domain of CaNdt80p is critical for its function in drug resistance in C. albicans.

scholarly journals The Yeast Heat Shock Transcription Factor Changes Conformation in Response to Superoxide and Temperature

2000 ◽  
Vol 11 (5) ◽  
pp. 1753-1764 ◽  
Author(s):  
Sengyong Lee ◽  
Tage Carlson ◽  
Noah Christian ◽  
Kristi Lea ◽  
Jennifer Kedzie ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Heat Shock ◽  
Dna Binding ◽  
Conformational Change ◽  
Mutational Analysis ◽  
Binding Domain ◽  
Heat Shock Transcription Factor ◽  
Dna Binding Domain ◽  
Yeast Saccharomyces Cerevisiae

In vitro DNA-binding assays demonstrate that the heat shock transcription factor (HSF) from the yeast Saccharomyces cerevisiae can adopt an altered conformation when stressed. This conformation, reflected in a change in electrophoretic mobility, requires that two HSF trimers be bound to DNA. Single trimers do not show this change, which appears to represent an alteration in the cooperative interactions between trimers. HSF isolated from stressed cells displays a higher propensity to adopt this altered conformation. Purified HSF can be stimulated in vitro to undergo the conformational change by elevating the temperature or by exposing HSF to superoxide anion. Mutational analysis maps a region critical for this conformational change to the flexible loop between the minimal DNA-binding domain and the flexible linker that joins the DNA-binding domain to the trimerization domain. The significance of these findings is discussed in the context of the induction of the heat shock response by ischemic stroke, hypoxia, and recovery from anoxia, all known to stimulate the production of superoxide.

Properties of the DNA-binding domain of the Saccharomyces cerevisiae STE12 protein

1991 ◽  
Vol 11 (12) ◽  
pp. 5910-5918 ◽  
Author(s):  
Y L Yuan ◽  
S Fields
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Amino Acids ◽  
Dna Binding ◽  
Binding Affinity ◽  
Binding Domain ◽  
Upstream Region ◽  
Dna Binding Domain ◽  
Yeast Saccharomyces Cerevisiae ◽  
Dnase I Footprinting

The STE12 protein of the yeast Saccharomyces cerevisiae binds to the pheromone response element (PRE) present in the upstream region of genes whose transcription is induced by pheromone. Using DNase I footprinting assays with bacterially made STE12 fragments, we localized the DNA-binding domain to 164 amino acids near the amino terminus. Footprinting of oligonucleotide-derived sequences containing one PRE, or two PREs in head-to-tail or tail-to-tail orientation, showed that the N-terminal 215 amino acids of STE12 has similar binding affinity to either of the dimer sites and a binding affinity 5- to 10-fold lower for the monomer site. This binding cooperativity was also evident on a fragment from the MFA2 gene, which encodes the a-factor pheromone. On this fragment, the 215-amino-acid STE12 fragment protected both a consensus PRE as well as a degenerate PRE containing an additional residue. Mutation of the degenerate site led to a 5- to 10-fold decrease in binding; mutation of the consensus site led to a 25-fold decrease in binding. The ability of PREs to function as pheromone-inducible upstream activation sequences in yeast correlated with their ability to bind the STE12 domain in vitro. The sequence of the STE12 DNA-binding domain contains similarities to the homeodomain, although it is highly diverged from other known examples of this motif. Moreover, the alignment between STE12 and the homeodomain postulates loops after both the putative helix 1 and helix 2 of the STE12 sequence.

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.

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