Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of yeast strains BY4743, Gis1delta and Rim15delta grown in ethanol- or glucose-limiting media

ABSTRACT: Cell growth is controlled by nutrients and growth factors. How cells are regulated to enter stationary phase is still poorly understood. Previously we have identified 17 yeast genes whose expression is significantly up-regulated following starvation for different macro-nutrients. Here we demonstrate that activation of some of these genes is dependent on the Rim15 kinase and the Gis1 transcription factor. Phenotypic and microarray analyses reveal that Rim15p and Gis1p have both overlapping and distinct functions suggesting a non-linear relationship between the two. Subsequently we demonstrate that independent of Rim15p, TOR controls the limited proteolysis of Gis1p and regulates the binding of functional fragments to their target promoters. The limited proteolysis of Gis1p is executed by the proteasome to prevent its target genes from over activation. Thus, TOR regulates the function of the proteasome in response to nutrients so that gene expression is properly controlled, not only during active growth, but also in stationary phase.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Andy Hayes

PROVIDER: E-MEXP-1139 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Gis1 is required for transcriptional reprogramming of carbon metabolism and the stress response during transition into stationary phase in yeast.

Zhang Nianshu N Wu Jian J Oliver Stephen G SG

Microbiology (Reading, England) 20090421 Pt 5

Transition from growth to the stationary phase in yeast is still poorly understood. Previously, we identified a group of yeast genes that are universally upregulated upon starvation for different macronutrients. Here, we demonstrate that the Gis1 transcription factor and the Rim15 kinase are responsible for the upregulation of many of these genes. In chemostat cultures, gis1 or rim15 mutant cells are outcompeted by their wild-type parents under conditions resembling the later stages of diauxie ( ...[more]

PMID: 19383711

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Project description:The Saccharomyces cerevisiae SFP1 is required for proper regulation of ribosome biogenesis and cell size in response to nutrients. A mutant deleted for SFP1 shows specific traits among which a slow growth phenotype, which is particularly evident during growth on glucose. To assess the effects of nutrients on the activity of Sfp1 independent by growth rate related feedback we grew an sfp1Î mutant and its isogenic reference strain in chemostat cultures, at the same specific growth rate, under glucose/ethanol-limitation. Our data show that Sfp1 is involved in the modulation of cell size and RiBi gene expression and that these two functions are differently influenced by nutrients. The continuous cultures were then pulsed with a glucose excess generating a situation of batch growth similar to shake flask cultures. The dynamic analysis of the metabolic and transcriptional response following the glucose addition suggested that Sfp1 plays a role at the crossroads of ribosome biogenesis and central carbon metabolism regulation. Finally, we show that the down-regulation of RP genes, which was observed in an sfp1Î strain during shake flask growth, cannot be directly ascribed to the absence of Sfp1 but is most probably a secondary effect due to the low growth potential of the mutant strain. Experiment Overall Design: After ten volume changes, few seconds after the samples for the steady state analysis were collected, the anaerobic glucose pulse experiments were started by sparging the medium reservoir and the fermenter with pure nitrogen gas (airflow of 0.5 L min-1, Hoek-Loos, Schiedam, <5 ppm O2). NorpreneTM tubing and butyl septa were used to minimize oxygen diffusion into the anaerobic culture. Two minutes after nitrogen sparging and just before the addition of glucose, the medium and the effluent pumps were switched off. At this time point (which we will refer to as time T=0) the 200 mM glucose pulse was injected aseptically through a rubber septum. Experiment Overall Design: Sampling from chemostats, total RNA extraction, probe preparation and hybridization to Affymetrix GenechipÂ® microarrays were performed as previously described (1). Samples were collected at steady state and then at 5, 10, 30, 60 and 120 minutes after the pulse. The results relative to steady state samples were derived from three independent cultures, those relative to the time course analysis were derived from two independent cultures. Experiment Overall Design: 1) Cipollina C., van den Brink J., Daran-Lapujade P., Pronk J.T., Vai M. and de Winde J.H. (2007) Revisiting the role of yeast Sfp1 in ribosome biogenesis and cell size control: A chemostat study. Microbiology. In press.

Dataset Information

Transcription profiling of yeast strains BY4743, Gis1delta and Rim15delta grown in ethanol- or glucose-limiting media

Publications

Gis1 is required for transcriptional reprogramming of carbon metabolism and the stress response during transition into stationary phase in yeast.

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