Project description:Investigation of the effects of genetically depleting eIF4G from yeast cells on global translational efficiencies, using gene expresssion microarrays to measure the abundance of mRNA in polysomes relative to total mRNA for ~5900 genes
Project description:Investigation of the effects of genetically depleting eIF4G from yeast cells on global translational efficiencies, using gene expresssion microarrays to measure the abundance of mRNA in polysomes relative to total mRNA for ~5900 genes Three biological replicates were examined (designated projects I, II, and III), representing heavy polysomes (HP), light polysomes (LP), and total RNA (T) preparations from three independent pairs of WT and eIF4G degron mutant cultures. Cy3-labeled cDNAs were generated from the 3 HP, 3 LP, and 3 total RNA samples prepared for each strain and the resulting 18 sets of cDNAs were used to probe three (technical) replicate whole-genome microarrays, containing multiple 60-mer oligonucleotides for each gene. The “normalized gene expression summary values” were calculated for each gene from the data obtained from the three technical replicates and used to calculate the translational efficiency (TE) of each gene as the ratio of the intensity values for HP to total RNA (HP/T) or LP to total RNA (LP/T) for each project.
Project description:The model yeast species Saccharomyces cerevisiae is used in many fundamental and applied research applications, including biosensors and production of many compounds. However, given the enormous work invested in the studies of yeast transcription response to various conditions, there are still substances not explored in this regard. In this work, we explore the transcriptional response of S. cerevisiae to a wide range of concentrations of the D-enantiomer of lactic acid and compare it to the response to L-lactic acid. Of these conditions, we only recorded a transcriptional response to the relatively high concentrations of DLA of 5 and 45 mM, as well as to 45 mM LLA. Our data did not reveal any natural yeast promoters that quantitatively sense D-lactic acid but provide the first description of the transcriptome-wide response to DLA, as well as enrich our understanding of the LLA response.
Project description:We performed ribosome profiling of wild-type and loc1- cells. We found that approximately 1500 genes exhibit increased translational efficiencies in the absence of Loc1, indicating that Loc1 is required for their translational repression. Examination of translational efficiencies by comparing ribosome footprints and mRNA abundances in two different cell lines.
Project description:Yeast is a powerful model system for studying the action of small molecule therapeutics. An important limitation has been low efficacy of many small molecules in yeast due to limited intracellular drug accumulation. We used the DNA binding domain of the pleiotropic drug resistance regulator Pdr1 fused in-frame to transcription repressors to repress Pdr1 regulated genes. Expression of these regulators conferred dominant enhancement of drug sensitivity and led to greatly diminished levels of Pdr1p regulated transcripts, including the yeast p-glycoprotein homologue Pdr5. Enhanced sensitivity was seen for a wide range of small molecules. Biochemical measurements demonstrated enhanced accumulation of rhodamine in yeast cells carrying the chimeras. These repressors of Pdr1p regulated transcripts can be introduced into large collections of strains such as the S. cerevisiae deletion set, and enhance the utility of yeast for studying drug action and for mechanism-based drug discovery. Keywords: Comparison of genetic variants
Project description:Proteotoxic stress triggers adaptive cellular responses, including changes in gene expression on the levels of transcription and translation. In this study, we analyzed the translational response of yeast cells to impaired protein import into mitochondria, a condition under which mitochondrial precursor proteins accumulate in the cytosol and impose proteotoxic stress. We analyzed changes in translational efficiency as well as more subtle changes in the distribution of ribosomes along transcripts, with a special focus on translation initiation sites.
