The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae

Teixeira, Miguel C.; Monteiro, Pedro T.; Jain, Pooja; Tenreiro, Sandra; Fernandes, Alexandra R.; Mira, Nuno P.; Alenquer, Marta; Freitas, Ana T.; Oliveira, Arlindo L.; Sá‐Correia, Isabel

doi:10.1093/nar/gkj013

Cited by 452 publications

(496 citation statements)

References 12 publications

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“…Also, in the case of the QDR2 promoter region, there is no established DNA binding site for Gcn4p [the sequence TGA(G/G)TCA]. Using the YEASTRACT database (http://www.yeastract.com) (43), five cis-acting replication element-like sequences were found. Since Gcn4p was proven to compete with Sko1p for these binding sites in the HAL1 promoter region (28), it is possible that they may also be used to bind Gcn4p to the QDR2 promoter region.…”

Section: Discussionmentioning

confidence: 99%

Saccharomyces cerevisiae Multidrug Resistance Transporter Qdr2 Is Implicated in Potassium Uptake, Providing a Physiological Advantage to Quinidine-Stressed Cells

et al. 2007

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The QDR2 gene of Saccharomyces cerevisiae encodes a putative plasma membrane drug:H ؉ antiporter that confers resistance against quinidine, barban, bleomycin, and cisplatin. This work provides experimental evidence of defective K ؉ (Rb ؉ ) uptake in the absence of QDR2. The direct involvement of Qdr2p in K ؉ uptake is reinforced by the fact that increased K ؉ (Rb ؉ ) uptake due to QDR2 expression is independent of the Trk1p/Trk2p system. QDR2 expression confers a physiological advantage for the yeast cell during the onset of K ؉ limited growth, due either to a limiting level of K ؉ in the growth medium or to the presence of quinidine. This drug decreases the K ؉ uptake rate and K ؉ accumulation in the yeast cell, especially in the ⌬qdr2 mutant. Qdr2p also helps to sustain the decrease of intracellular pH in quinidine-stressed cells in growth medium at pH 5.5 by indirectly promoting H ؉ extrusion affected by the drug. The results are consistent with the hypothesis that Qdr2p may also couple K ؉ movement with substrate export, presumably with quinidine. Other clues to the biological role of QDR2 in the yeast cell come from two additional lines of experimental evidence. First, QDR2 transcription is activated under nitrogen (NH 4 ؉ ) limitation or when the auxotrophic strain examined enters stationary phase due to leucine limitation, this regulation being dependent on general amino acid control by Gcn4p. Second, the amino acid pool is higher in ⌬qdr2 cells than in wild-type cells, indicating that QDR2 expression is, directly or indirectly, involved in amino acid homeostasis.

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Section: Discussionmentioning

confidence: 99%

Saccharomyces cerevisiae Multidrug Resistance Transporter Qdr2 Is Implicated in Potassium Uptake, Providing a Physiological Advantage to Quinidine-Stressed Cells

et al. 2007

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“…Restriction sites were removed by introducing point mutations, using assembly PCR. Mutations were chosen such that they are silent in coding sequences and not interfering with known transcription factor binding sites in promoter regions, as evaluated by the YEASTTRACT database (Teixeira et al, 2006). The other plasmids of the pRG series were generated by exchanging vector parts using restriction enzymes and T4 DNA ligase (New England BioLabs, USA).…”

Section: Plasmid Constructionmentioning

confidence: 99%

A shuttle vector series for precise genetic engineering of Saccharomyces cerevisiae

Gnügge

Liphardt

Rudolf

2016

Yeast

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Shuttle vectors allow for an efficient transfer of recombinant DNA into yeast cells and are widely used in fundamental research and biotechnology. While available shuttle vectors are applicable in many experimental settings, their use in quantitative biology is hampered by insufficient copy number control. Moreover, they often have practical constraints, such as limited modularity and few unique restriction sites. We constructed the pRG shuttle vector series, consisting of single-and multi-copy integrative, centromeric and episomal plasmids with marker genes for the selection in all commonly used auxotrophic yeast strains. The vectors feature a modular design and a large number of unique restriction sites, enabling an efficient exchange of every vector part and expansion of the series. Integration into the host genome is achieved using a double-crossover recombination mechanism, resulting in stable single-and multi-copy modifications. As centromeric and episomal plasmids give rise to a heterogeneous cell population, an analysis of their copy number distribution and loss behaviour was performed. Overall, the shuttle vector series supports the efficient cloning of genes and their maintenance in yeast cells with improved copy number control.

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“…The glutathione deletion mutant gsh1Δ was therefore sensitive to 56MESS. a Motifs were obtained from analysis of promoter regions of 56MESS up-regulated genes using RSA tools [70] b Minus log transform of the E-value, which is the product of multiplying the p-value by the number of distinct motifs. The p-value is a probability of chance occurrence of particular motifs in the promoter regions of a given list of genes.…”

Section: Role Of Glutathione In 56mess Cytotoxicitymentioning

confidence: 99%

Identification of the molecular mechanisms underlying the cytotoxic action of a potent platinum metallointercalator

et al. 2011

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Platinum-based DNA metallointercalators are structurally different from the covalent DNA binders such as cisplatin and its derivatives but have potent in vitro activity in cancer cell lines. However, limited understanding of their molecular mechanisms of cytotoxic action greatly hinders their further development as anticancer agents. In this study, a lead platinum-based metallointercalator, [(5,6-dimethyl-1,10-phenanthroline) (1S,2S-diaminocyclohexane) platinum(II)] 2+ (56MESS) was found to be 163-fold more active than cisplatin in a cisplatin-resistant cancer cell line. By using transcriptomics in a eukaryotic model organism, yeast Saccharomyces cerevisiae, we identified 93 genes that changed their expressions significantly upon exposure of 56MESS in comparison to untreated controls (p≤0.05). Bioinformatic analysis of these genes demonstrated that iron and copper metabolism, sulfur-containing amino acids and stress response were involved in the cytotoxicity of 56MESS. Follow-up experiments showed that the iron and copper concentrations were much lower in 56MESS-treated cells compared to controls as measured by inductively coupled plasma optical emission spectrometry. Deletion mutants of the key genes in the iron and copper metabolism pathway and glutathione synthesis were sensitive to 56MESS. Taken together, the study demonstrated that the cytotoxic action of 56MESS is mediated by its ability to disrupt iron and copper metabolism, suppress the biosynthesis of sulfur-containing amino acids and attenuate cellular defence capacity. As these mechanisms are in clear contrast to the DNA binding mechanism for cisplatin and its derivative, 56MESS may be able to overcome cisplatinresistant cancers. These findings have provided basis to further develop the platinum-based metallointercalators as anticancer agents.

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The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae

Cited by 452 publications

References 12 publications

Saccharomyces cerevisiae Multidrug Resistance Transporter Qdr2 Is Implicated in Potassium Uptake, Providing a Physiological Advantage to Quinidine-Stressed Cells

Saccharomyces cerevisiae Multidrug Resistance Transporter Qdr2 Is Implicated in Potassium Uptake, Providing a Physiological Advantage to Quinidine-Stressed Cells

A shuttle vector series for precise genetic engineering of Saccharomyces cerevisiae

Identification of the molecular mechanisms underlying the cytotoxic action of a potent platinum metallointercalator

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