Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of yeast treated with rapamycin in a 7-part time series

ABSTRACT: This experiment was a 7-part time series (or, 2x7 factorial design) examining the effect of rapamycin on gene expression in Saccharomyces cerevisiae. Treated and untreated cultures were compared at 0, 20, 40, 60, 120, 240, and 360 minutes. In the paper, expression ratios (mRNA) at each time point were compared to equivalent ratios (protein) from shotgun proteomics NSAF data. High-expressing mRNA ratios were also clustered and GO-characterized.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Ariel Paulson

PROVIDER: E-TABM-639 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Delayed correlation of mRNA and protein expression in rapamycin-treated cells and a role for Ggc1 in cellular sensitivity to rapamycin.

Fournier Marjorie L ML Paulson Ariel A Pavelka Norman N Mosley Amber L AL Gaudenz Karin K Bradford William D WD Glynn Earl E Li Hua H Sardiu Mihaela E ME Fleharty Brian B Seidel Christopher C Florens Laurence L Washburn Michael P MP

Molecular & cellular proteomics : MCP 20091110 2

To identify new molecular targets of rapamycin, an anticancer and immunosuppressive drug, we analyzed temporal changes in yeast over 6 h in response to rapamycin at the transcriptome and proteome levels and integrated the expression patterns with functional profiling. We show that the integration of transcriptomics, proteomics, and functional data sets provides novel insights into the molecular mechanisms of rapamycin action. We first observed a temporal delay in the correlation of mRNA and prot ...[more]

PMID: 19955083

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Project description:Background: Malaria is a one of the most important infectious diseases and is caused by parasitic protozoa of the genus Plasmodium. Previously, the quantitative characterization of the P. falciparum transcriptome demonstrated that the strictly controlled progression of these parasites through their intra-erythrocytic developmental cycle is accompanied by a continuous cascade of gene expression. Although such analyses have proven immensely useful, the precise correlations between transcript and protein abundance remain under-scrutinized. Results: Here, we present a quantitative time-course analysis of relative protein abundance for schizont-stage parasites (34-46 hours post-invasion) based on 2D-gel electrophoresis of protein samples labeled with DIGE fluorescent dyes. For this purpose we analyzed parasite samples taken at four-hour intervals from a tightly synchronized culture and established more than 500 individual protein abundance profiles with high temporal resolution and quantitative reproducibility. Approximately half of all profiles exhibit a significant change in abundance and 12% display an expression peak during the observed 12-hour time interval. Intriguingly, identification of 54 protein spots by mass spectrometry revealed that 58% of the corresponding proteins including actin-I, enolase, eIF4A, eIF5A, and several heat shock proteins are represented by more than one isoform, presumably due to post-translational modifications, with the various isoforms of a given protein frequently showing different expression patterns. Furthermore, comparisons with transcriptome data generated from the same parasite samples reveal significant post-transcriptional gene expression regulation. Conclusions: Together, our data indicate that both post-transcriptional and post-translational events are widespread and of presumably great biological significance during the intra-erythrocytic development of P. falciparum. Additional comment: In essence, the microarray data generated in this study is a repeat of the transcriptome analysis described in Bozdech et al., PLoS Biol 2003, 1(1):E5. Differences include (1) an improved set of oligonucleotides [see Hu et al., BMC Bioinformatics 2007, 8:350] used in the study associated with this GEO entry, and (2) the sampling at only four timepoints during the intra-erythrocytic development cycle (schizont stage) to match and complement the samples processed in the concomitant proteomics analysis. Four timepoint samples were harvested from a tightly synchronized 6 liter biofermenter culture of P. falciparum during schizont stage (at 34, 38, 42, and 46 hours post-invasion) and compared against a 3D7 RNA reference pool.

Dataset Information

Transcription profiling of yeast treated with rapamycin in a 7-part time series

Publications

Delayed correlation of mRNA and protein expression in rapamycin-treated cells and a role for Ggc1 in cellular sensitivity to rapamycin.

Similar Datasets

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