scholarly journals Transcription Factor–DNA Binding Motifs in Saccharomyces cerevisiae: Tools and Resources

2016 ◽  
Vol 2016 (11) ◽  
pp. pdb.top080622 ◽  
Author(s):  
Joshua L. Schipper ◽  
Raluca M. Gordân
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Transcription Factor ◽  
Dna Binding ◽  
Binding Motifs ◽  
Dna Binding Motifs

scholarly journals xUBF, an RNA polymerase I transcription factor, binds crossover DNA with low sequence specificity.

1994 ◽  
Vol 14 (5) ◽  
pp. 2871-2882 ◽  
Author(s):  
C H Hu ◽  
B McStay ◽  
S W Jeong ◽  
R H Reeder
Keyword(s):  
Transcription Factor ◽  
Dna Binding ◽  
Rna Polymerase ◽  
Rna Polymerase I ◽  
Intact Protein ◽  
Sequence Specificity ◽  
Binding Motifs ◽  
Double Helices ◽  
Dna Binding Motifs ◽  
Polymerase I

Xenopus UBF (xUBF) is a transcription factor for RNA polymerase I which contains multiple DNA-binding motifs. These include a short basic region adjacent to a dimer motif plus five high-mobility-group (HMG) boxes. All of these DNA-binding motifs exhibit low sequence specificity, whether assayed singly or together. In contrast, the HMG boxes recognize DNA structure that is formed when two double helices are crossed over each other. HMG box 1, in particular, requires association of two double helices before it will bind and, either by itself or in the context of the intact protein, will loop DNA and organize it into higher-order structures. We discuss how this mode of binding affects the function of xUBF as a transcription factor.

scholarly journals The Type III Effector HsvG of the Gall-Forming Pantoea agglomerans Mediates Expression of the Host Gene HSVGT

2012 ◽  
Vol 25 (2) ◽  
pp. 231-240 ◽  
Author(s):  
Gal Nissan ◽  
Shulamit Manulis-Sasson ◽  
Laura Chalupowicz ◽  
Doron Teper ◽  
Adva Yeheskel ◽  
...  
Keyword(s):  
Amino Acids ◽  
Transcription Factor ◽  
Dna Binding ◽  
Leucine Zipper ◽  
Pantoea Agglomerans ◽  
In Planta ◽  
Binding Motifs ◽  
Type Iii Effector ◽  
Type Iii ◽  
Dna Binding Motifs

The type III effector HsvG of the gall-forming Pantoea agglomerans pv. gypsophilae is a DNA-binding protein that is imported to the host nucleus and involved in host specificity. The DNA-binding region of HsvG was delineated to 266 amino acids located within a secondary structure region near the N-terminus of the protein but did not display any homology to canonical DNA-binding motifs. A binding site selection procedure was used to isolate a target gene of HsvG, named HSVGT, in Gypsophila paniculata. HSVGT is a predicted acidic protein of the DnaJ family with 244 amino acids. It harbors characteristic conserved motifs of a eukaryotic transcription factor, including a bipartite nuclear localization signal, zinc finger, and leucine zipper DNA-binding motifs. Quantitative real-time polymerase chain reaction analysis demonstrated that HSVGT transcription is specifically induced in planta within 2 h after inoculation with the wild-type P. agglomerans pv. gypsophilae compared with the hsvG mutant. Induction of HSVGT reached a peak of sixfold at 4 h after inoculation and progressively declined thereafter. Gel-shift assay demonstrated that HsvG binds to the HSVGT promoter, indicating that HSVGT is a direct target of HsvG. Our results support the hypothesis that HsvG functions as a transcription factor in gypsophila.

scholarly journals Induction of meiosis in Saccharomyces cerevisiae depends on conversion of the transcriptional represssor Ume6 to a positive regulator by its regulated association with the transcriptional activator Ime1.

1996 ◽  
Vol 16 (5) ◽  
pp. 2518-2526 ◽  
Author(s):  
I Rubin-Bejerano ◽  
S Mandel ◽  
K Robzyk ◽  
Y Kassir
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Protein Kinase ◽  
Dna Binding ◽  
Budding Yeast ◽  
Transcriptional Activator ◽  
Dna Binding Protein ◽  
Activation Domain ◽  
Yeast Saccharomyces Cerevisiae ◽  
Binding Motifs ◽  
Dna Binding Motifs

The transcription of meiosis-specific genes, as well as the initiation of meiosis, in the budding yeast Saccharomyces cerevisiae depends on IME1. IME1 encodes a transcriptional activator which lacks known DNA binding motifs. In this study we have determined the mode by which Ime1 specifically activates the transcription of meiotic genes. We demonstrate that Ime1 is recruited to the promoters of meiotic genes by interacting with a DNA-binding protein, Ume6. This association between Ime1 and Ume6 depends on both starvation and the activity of a protein kinase, encoded by RIM11 In the absence of Ime1, Ume6 represses the transcription of meiotic genes. However, in the presence of Ime1, or when Ume6 is fused in frame to the Gal4 activation domain, Ume6 is converted from a repressor to an activator, resulting in the transcription of meiosis-specific genes and the formation of asci.

scholarly journals Rice protein-binding microarrays: a tool to detect cis-acting elements near promoter regions in rice

Planta ◽  
2021 ◽  
Vol 253 (2) ◽  
Author(s):  
Joung Sug Kim ◽  
SongHwa Chae ◽  
Kyong Mi Jun ◽  
Gang-Seob Lee ◽  
Jong-Seong Jeon ◽  
...  
Keyword(s):  
Dna Binding ◽  
Protein Binding ◽  
Gene Networks ◽  
Upstream Region ◽  
Transcriptional Level ◽  
Cis Elements ◽  
Promoter Regions ◽  
Entire Genome ◽  
Binding Motifs ◽  
Dna Binding Motifs

Abstract Main conclusion The present study showed that a rice (Oryza sativa)-specific protein-binding microarray (RPBM) can be applied to analyze DNA-binding motifs with a TF where binding is evaluated in extended natural promoter regions. The analysis may facilitate identifying TFs and their downstream genes and constructing gene networks through cis-elements. Abstract Transcription factors (TFs) regulate gene expression at the transcriptional level by binding a specific DNA sequence. Thus, predicting the DNA-binding motifs of TFs is one of the most important areas in the functional analysis of TFs in the postgenomic era. Although many methods have been developed to address this challenge, many TFs still have unknown DNA-binding motifs. In this study, we designed RPBM with 40-bp probes and 20-bp of overlap, yielding 49 probes spanning the 1-kb upstream region before the translation start site of each gene in the entire genome. To confirm the efficiency of RPBM technology, we selected two previously studied TFs, OsWOX13 and OsSMF1, and an uncharacterized TF, OsWRKY34. We identified the ATTGATTG and CCACGTCA DNA-binding sequences of OsWOX13 and OsSMF1, respectively. In total, 635 and 932 putative feature genes were identified for OsWOX13 and OsSMF1, respectively. We discovered the CGTTGACTTT DNA-binding sequence and 195 putative feature genes of OsWRKY34. RPBM could be applicable in the analysis of DNA-binding motifs for TFs where binding is evaluated in the promoter and 5′ upstream CDS regions. The analysis may facilitate identifying TFs and their downstream genes and constructing gene networks through cis-elements.

The orientation and spacing of core DNA-binding motifs dictate selective transcriptional responses to three nuclear receptors

Cell ◽  
1991 ◽  
Vol 65 (7) ◽  
pp. 1267-1279 ◽  
Author(s):  
Anders M. Näär ◽  
Jean-Marle Boutin ◽  
Steven M. Lipkin ◽  
Victor C. Yu ◽  
Jeffrey M. Holloway ◽  
...  
Keyword(s):  
Dna Binding ◽  
Nuclear Receptors ◽  
Transcriptional Responses ◽  
Binding Motifs ◽  
Dna Binding Motifs

Intrinsic Fluoride Tolerance Regulated by a Transcription Factor

2020 ◽  
Vol 99 (11) ◽  
pp. 1270-1278
Author(s):  
M. Lu ◽  
Z. Xiang ◽  
T. Gong ◽  
X. Zhou ◽  
Z. Zhang ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Inhibitory Concentration ◽  
Transcriptional Regulator ◽  
Mutant Library ◽  
Mobility Shift ◽  
Binding Motifs ◽  
Dnase I Footprinting ◽  
Dna Binding Motifs ◽  
Dental Hard Tissues ◽  
Planktonic State

Fluoride facilitates the remineralization of dental hard tissues and affects bacterial activities. Therefore, it is extensively used as an anti-caries agent in clinical practice and daily life. Although some studies focused on understanding Streptococcus mutans’ response to fluoride, the mechanism regulating intrinsic fluoride tolerance is not yet clear. Since the TetR family of transcription factors is associated with multidrug resistance, our aim was to evaluate whether they are related to fluoride tolerance in S. mutans. A mutant library including each S. mutans TetR gene was constructed and the transcription factor fluoride related transcriptional regulator (FrtR) was identified. The in-frame deletion of the S. mutans frtR gene resulted in decreased cell viability under fluoride in both the planktonic state and single-/dual-species biofilms. This in-frame frtR mutant was used for RNA-sequencing and the fluoride related permease gene ( frtP) was found as 1 of the downstream genes directly regulated by FrtR. The recombinant FrtR protein was purified, and conserved DNA binding motifs were determined using electrophoretic mobility shift and DNase I footprinting assays. Finally, a series of mutant and complement strains were constructed to perform the minimum inhibitory concentration (MIC) assays, which indicated that frtP upregulation led to the increase of fluoride sensitivity. Collectively, our results indicate that FrtR is an important transcription factor regulating the frtP expression in S. mutans, thus affecting the intrinsic fluoride tolerance. Therefore, this study provides novel insights into a potential target to increase the S. mutans sensitivity to fluoride for a better prevention of dental caries.

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