Project description:Cellular differentiation is driven by coordinately regulated changes in gene expression. Translational control of gene expression is increasingly recognized as pervasive and quantitatively significant, but the mechanisms responsible for widespread changes in gene-specific translation activity are largely unknown. Here we investigate the mechanisms responsible for translational reprogramming during cellular adaptation to the absence of glucose, a stimulus that induces invasive filamentous differentiation in yeast. We show that gene-specific translation efficiencies are highly adapted to cellular conditions and that glucose withdrawal is accompanied by widespread translational reprogramming at the level of translation initiation. We demonstrate that transcripts from <5% of genes make up the majority of translating mRNA in both rapidly dividing and starved cells. Moreover, the identities of these highly translated genes are growth-state specific, and they are subject to condition-dependent translational privilege. By comparing glucose starvation to other growth-attenuating stresses, we distinguish a glucose-specific translational response that regulates ribosomal protein and mitochondrial protein-coding genes. This response is mediated through signaling by protein kinase A (PKA). These findings reveal a high degree of growth-state specialization of the translatome and identify PKA as an important regulator of gene-specific translation activity. Examine translational adaptation in yeast in response to glucose starvation
Project description:In the yeast Saccharomyces cerevisiae, accumulation of misfolded proteins in the endoplasmic reticulum (ER) causes ER stress and activates the unfolded protein response (UPR) mediated by Hac1p, whereas the heat shock response (HSR) mediated by Hsf1p mainly regulates cytosolic processes and protects the cell from different stresses. In this study, we find that a constitutive activation of the HSR by over-expression of a mutant HSF1 gene could relieve ER stress in both wild type and hac1∆ UPR-deficient cells. We studied the genome-wide transcriptional response in order to identify regulatory mechanisms that govern the interplay between UPR and HSR responses. Interestingly, we find that the regulation of ER stress via HSR is mainly through facilitation of protein folding and secretion and not via the induction of Rpn4-dependent proteasomal activity.
Project description:This SuperSeries is composed of the following subset Series: GSE38565: The yeast PP2A-CDC55 phosphatase regulates the transcriptional response to hyperosmolarity stress by regulating Msn2 and Msn4 [Time course 1] GSE42033: The yeast PP2A-CDC55 phosphatase regulates the transcriptional response to hyperosmolarity stress by regulating Msn2 and Msn4 [Time course 2] Refer to individual Series
Project description:The yeast PP2A-Cdc55 Serine/Threonine phosphatase regulates transcription under certain conditions. It is required for full activation of the environmental stress response mediated by the transcription factors Msn2 and Msn4. PP2A-Cdc55 contributes to sustained nuclear accumulation of Msn2 and Msn4 and extended chromatin recruitment under stress conditions such as hyperosmolarity stress. Transcript profiles of Msn2 and Msn4 double mutants are similar to cdc55 and the corresponding triple mutants. This argues for a Msn2/4 specific function of PP2A-Cdc55. Time course of 10 20 and 30 minutes hyperosmolarity treated yeast cells of wild type (W303), msn2msn4, cdc55, msn2msn5cdc55 genetic background.
Project description:In the yeast Saccharomyces cerevisiae, accumulation of misfolded proteins in the endoplasmic reticulum (ER) causes ER stress and activates the unfolded protein response (UPR) mediated by Hac1p, whereas the heat shock response (HSR) mediated by Hsf1p mainly regulates cytosolic processes and protects the cell from different stresses. In this study, we find that a constitutive activation of the HSR by over-expression of a mutant HSF1 gene could relieve ER stress in both wild type and hac1delta UPR-deficient cells. We studied the genome-wide transcriptional response in order to identify regulatory mechanisms that govern the interplay between UPR and HSR responses. Interestingly, we find that the regulation of ER stress via HSR is mainly through facilitation of protein folding and secretion and not via the induction of Rpn4-dependent proteasomal activity. Four Saccharomyces cerevisiae strains, WT, WT(hsf1), hac1delta and hac1delta(hsf1), were grown in SD-URA medium and treated with 2.5 mM DTT. After two hours induction, samples were taken for RNA extraction and hybridization on Affymetrix microarrays. Biological triplicates were applied.
Project description:The yeast PP2A-Cdc55 Serine/Threonine phosphatase regulates transcription under certain conditions. It is required for full activation of the environmental stress response mediated by the transcription factors Msn2 and Msn4. PP2A-Cdc55 contributes to sustained nuclear accumulation of Msn2 and Msn4 and extended chromatin recruitment under stress conditions such as hyperosmolarity stress. Transcript profiles of Msn2 and Msn4 double mutants are similar to cdc55 and the corresponding triple mutants. This argues for a Msn2/4 specific function of PP2A-Cdc55. Time course of 0, 10 20 and 30 minutes hyperosmolarity treated yeast cells of msn2msn4 or msn2msn4cdc55 genetic background, both carrying plasmid pMsn2pMsn2DNES; reference hybridization: untreated W303 msn2msn4 pMsn2pMsn2DNES labelled with Cy3
Project description:The SWI/SNF ATP-dependent chromatin remodeler is a master regulator of the epigenome; controlling pluripotency, cell fate determination and differentiation. There is a sparsity of information on the autoregulation of SWI/SNF, the domains involved and their mode of action. We find a DNA or RNA binding module conserved from yeast to humans located in the C-terminus of the catalytic subunit of SWI/SNF called the AT-hook that positively regulates the chromatin remodeling activity of yeast and mouse SWI/SNF. The AT-hook in yeast SWI/SNF interacts with the SnAC and ATPase domains, which after binding to nucleosome switches to contacting the N-terminus of histone H3. Deletion of the AT-hooks in yeast SWI/SNF and mouse esBAF complexes reduces the remodeling activity of SWI/SNF without affecting complex integrity or its recruitment to nucleosomes. In addition, deletion of the AT-hook impairs the ATPase and nucleosome mobilizing activities of yeast SWI/SNF without disrupting the interactions of the ATPase domain with nucleosomal DNA. The AT-hook is also important in vivo for SWI/SNF-dependent response to amino acid starvation in yeast and for cell lineage priming in mouse embryonic stem cells. In summary, the AT-hook is shown to be an evolutionarily conserved autoregulatory domain of SWI/SNF that positively regulates SWI/SNF both in vitro and in vivo.
Project description:In fungal species, differentiation to the filamentous/hyphal cell type is critical for entry into host cells and virulence. Comparative RNA sequencing was used to explore the pathways that regulate differentiation to the filamentous cell type in yeast. This approach uncovered a role for the stress-response MAPK pathway, HOG, during the increased metabolic respiration that induces filamentous growth. In this context, the AMPK Snf1p and ER stress kinase Ire1p regulated the HOG pathway. Cross-modulation between the HOG and filamentous growth (ERK-type) MAPK pathways optimized the differentiation response. The regulatory circuit described here may extend to behaviors in metazoans. Comparison of expression patterns of wild-type and mutant yeast cells grown in salt, tunicamycin or galactose by comparative RNA sequencing analysis.