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Expression data from yeast cells with pop2 deletion and overexpressing STM1 or STM1 R237K mutant

ABSTRACT: A880 has pop2 deletion and a very slow-growth phenotype with glycerol as carbon source. A880 transformed with 2-micron plasmids encoding STM1 can grow robustly on glycerol plates. The Arg237 on Stm1p can be methylated by Hmt1p. A880 transformed with 2-micron plasmids encoding the Stm1p R237K mutant retain the slow-growth phenotype on glycerol plates. We used microarrays to assess the transcription profiles of A880, and A880 transformed with STM1 or STM1 R237K mutant. The goal is to identify genes that are up- or down-regulated in the presence of STM1 R237K mutant but not in the presence of the wild type STM1.

ORGANISM(S): Schizosaccharomyces pombe Saccharomyces cerevisiae

PROVIDER: GSE28794 | GEO | 2011/04/22

SECONDARY ACCESSION(S): PRJNA138811

REPOSITORIES: GEO

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Expression data from yeast cells with pop2 deletion and overexpressing STM1 or STM1 R237K mutant

Project description:A880 has pop2 deletion and a very slow-growth phenotype with glycerol as carbon source. A880 transformed with 2-micron plasmids encoding STM1 can grow robustly on glycerol plates. The Arg237 on Stm1p can be methylated by Hmt1p. A880 transformed with 2-micron plasmids encoding the Stm1p R237K mutant retain the slow-growth phenotype on glycerol plates. We used microarrays to assess the transcription profiles of A880, and A880 transformed with STM1 or STM1 R237K mutant. The goal is to identify genes that are up- or down-regulated in the presence of STM1 R237K mutant but not in the presence of the wild type STM1. BY4741 (wild type control), A880 (BY4741 with pop2 deletion), A880STM1 (A880 transformed with STM1) and A880STM1K (A880 transformed with STM1 carrying an Arg237 to lysine substitution) cells were grown in SC medium with glucose as carbon source to early log phase. The cells were shifted to SC medium containing 2% glycerol and incubated for 12 hours before harvesting. Total RNAs were extracted for microarray analysis. Two data sets were generated from separate experiments and cell cultures.

2011-04-22 | E-GEOD-28794 | biostudies-arrayexpress

ler vs pop2-1: gaba over-accumulation effects-Transcriptomic analysis of pop2-1 mutant in Arabidopsis thaliana

Project description:au05-03_gaba - ler vs pop2-1: gaba over-accumulation effects - The analysis aims at identifying genes that are differentially regulated by the over-accumulation of GABA observed in the mutant pop2-1 in response to treatment with exogenous GABA and that may explain the singular phenotype of the mutant in this condition. Designed experiment consisted in comparison of transcriptomes of Arabidopsis thaliana Landsberg erecta ecotype and its mutant pop2-1 (impaired in GABA transaminase activity) during a kinetic of endogenous GABA accumulation. For this purpose, 10-day-old plants grown on half strength Hoagland's agar medium were transferred to agar plates supplemented with 1 mM GABA. We isolated RNA from plants treated for 0, 1 and 4 days. Treatments were made in duplicate. Keywords: gene knock-out, time course

2009-04-11 | GSE11129 | GEO

ler vs pop2-1: gaba over-accumulation effects-Transcriptomic analysis of pop2-1 mutant in Arabidopsis thaliana

2009-04-11 | E-GEOD-11129 | biostudies-arrayexpress

Expression data from wt, pop2, pbp1, and mpt5-deletion yeast cells.

Project description:The S. cerevisiae Pop2 protein is an exonuclease in the Ccr4-Not complex that is a conserved regulator of gene expression. Pop2 regulates gene expression post-transcriptionally by shortening the poly(A) tail of mRNA. A previous study has shown that Pop2 is phosphorylated at threonine 97 (T97) by Yak1 protein kinase in response to glucose limitation. However, the physiological importance of Pop2 phosphorylation remains unknown. In this study, we found that Pop2 is phosphorylated at serine 39 (S39) under unstressed conditions. The dephosphorylation of S39 was occurred within 1 min after glucose depletion, and the addition of glucose to the glucose-deprived culture recovered this phosphorylation, suggesting that Pop2 phosphorylation at S39 is regulated by glucose. We previously reported that Pop2 takes a part in the cell wall integrity pathway by regulation of LRG1 mRNA; however, S39 phosphorylation of Pop2 is not involved in LRG1 expression. On the other hand, Pop2 phosphorylation at S39 is involved in the expression of HSP12 and HSP26, encoding small heat shock proteins. In medium supplemented with glucose, Pop2 might be phosphorylated at S39 by Pho85 kinase to repress the expression of HSP12 and HSP26. Glucose starvation inactivated Pho85, which resulted in the derepression of HSP12 and HSP26. Thus, Pop2 phosphorylation at S39 is important for Pop2 to repress the expression of stress response genes, HSP12 and HSP26, in the presence of glucose. Our results suggest that Pop2 phosphorylation by Pho85 kinase is a part of the glucose sensing system in yeast.

2019-03-01 | GSE124908 | GEO

ler vs pop2-1: gaba over-accumulation effects-Transcriptomic analysis of pop2-1 mutant in Arabidopsis thaliana

Project description:ler vs pop2-1: gaba over-accumulation effects-Transcriptomic analysis of pop2-1 mutant in Arabidopsis thaliana

| PRJNA106913 | ENA

Gene expression data from Arabidopsis wild-type and pop2-1 mutant flowers

Project description:Although two genes responsive to GABA were characterized previously in plants (Kathiresan et al 1997), a comprehensive study in reproductive and vegetative tissues has not been performed. Consequently, genes that mediate GABA response in plants remain unknown. We therefore used microarrays to survey the genome, identifying genes modulated in response to GABA in reproductive tissues. Flowers were collected as described in the protocols section for RNA extraction and hybridization on Affymetrix ATH1 Genechip microarrays. Gene expression in wild-type and pop2-1 mutant flowers containing high levels of endogenous GABA were compared.

2010-06-16 | E-GEOD-21945 | biostudies-arrayexpress

Expression data from S. cerevisiae, S288C with graded GCN5 F221A

Project description:S288C was transformed with plasmids expressing the GCN5 F221A mutant at varying levels. We sought to examine the global impact on gene expression using the Affymetrix yeast 2.0 arrays.

2012-05-03 | GSE26923 | GEO

Cell wall integrity is linked to mitochondria and phospholipid homeostasis in Candida albicans through the activity of the post-transcriptional regulator Ccr4-Pop2

Project description:The cell wall is essential for viability of fungi and is an effective drug target in pathogens such as Candida albicans. The contribution of posttranscriptional gene regulators to cell wall integrity in C. albicans is unknown. We show that the C. albicans Ccr4-Pop2 mRNA deadenylase, a regulator of mRNA stability and translation, is required for cell wall integrity. The ccr4/pop2 mutants display reduced wall β-glucans and sensitivity to the echinocandin caspofungin. Moreover, the deadenylase mutants are compromised for filamentation and virulence. We demonstrate that defective cell walls in the ccr4/pop2 mutants are linked to dysfunctional mitochondria and phospholipid imbalance. To further understand mitochondrial function in cell wall integrity, we screened a Saccharomyces cerevisiae collection of mitochondrial mutants. We identify several mitochondrial proteins required for caspofungin tolerance and find a connection between mitochondrial phospholipid homeostasis and caspofungin sensitivity. We focus on the mitochondrial outer membrane SAM complex subunit Sam37, demonstrating it is required for both trafficking of phospholipids between the ER and mitochondria and cell wall integrity. Moreover, in C. albicans also Sam37 is essential for caspofungin tolerance. Our study provides the basis for an integrative view of mitochondrial function in fungal cell wall biogenesis and resistance to echinocandin antifungal drugs.

2010-12-10 | GSE25891 | GEO

Cell wall integrity is linked to mitochondria and phospholipid homeostasis in Candida albicans through the activity of the post-transcriptional regulator Ccr4-Pop2

2010-12-10 | E-GEOD-25891 | biostudies-arrayexpress

miRNA profile of WI-38 cells and their progressively transformed derivatives

Project description:microRNA array of 4 cell lines: WI-38 primary fibroblasts (“Control”), slow growers (early passage after immortalization, Slow), fast growers (extensive passaging after immortalization) and fast growers transformed by constitutively activated mutant H-RasV12 (“Ras”)

2016-01-29 | GSE77338 | GEO

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