Similar Datasets
Project description:Gcr1, the most important transcription factor for glycolytic genes in Saccharomyces cerevisiae, was recently revealed to have two isoforms, Gcr1(U) and Gcr1(S), produced from unspliced and spliced transcripts, respectively. We generated strains expressing only Gcr1(U) or Gcr1(S) form using the CRISPR/Cas9 system, and added a TAP tag protein to the Gcr1(U) and Gcr1(S), using HIS3MX6 marker system. We conducted ChIP-seq for both strains during the glycolytic phase or after the diauxic shift.
2020-07-07 | GSE153841 | GEO
Project description:Gcr1, the most important transcription factor for glycolytic genes in Saccharomyces cerevisiae, was recently revealed to have two isoforms, Gcr1(U) and Gcr1(S), produced from unspliced and spliced transcripts, respectively. We generated strains expressing only Gcr1(U) or Gcr1(S) form using the CRISPR/Cas9 system, and performed RNA-seq for the two strains. Since Gcr1 works as a glycolytic gene transcription factor, we extracted whole RNA at the exponential phase (6 hrs after incubation) and the diauxic shift (12 hrs after incubation).
2020-07-07 | GSE153842 | GEO
Project description:To determine where Tup1 binds to chromatin during log phase, diauxic shift and stationary phase, we performed ChIP-seq.
2022-08-17 | GSE210932 | GEO
Project description:When bacteria grow in a medium with two sugars, they first use the preferred sugar and only then start metabolizing the second one. After the first exponential growth phase, a short lag phase of nongrowth is observed, a period called the diauxie lag phase. It is commonly seen as a phase in which the bacteria prepare themselves to use the second sugar. Here we reveal that, in contrast to the established concept of metabolic adaptation in the lag phase, two stable cell types with alternative metabolic strategies emerge and coexist in a culture of the bacterium Lactococcus lactis. Only one of them continues to grow. The fraction of each metabolic phenotype depends on the level of catabolite repression and the metabolic state-dependent induction of stringent response, as well as on epigenetic cues. Furthermore, we show that the production of alternative metabolic phenotypes potentially entails a bet-hedging strategy. This study sheds new light on phenotypic heterogeneity during various lag phases occurring in microbiology and biotechnology and adjusts the generally accepted explanation of enzymatic adaptation proposed by Monod and shared by scientists for more than half a century.
| S-EPMC4034238 | biostudies-other
Project description:BackgroundChromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) can locate transcription factor binding sites on genomic scale. Although many models and programs are available to call peaks, none has dominated its competition in comparison studies.ResultsWe propose a rigorous statistical model, the normal-exponential two-peak (NEXT-peak) model, which parallels the physical processes generating the empirical data, and which can naturally incorporate mappability information. The model therefore estimates total strength of binding (even if some binding locations do not map uniquely into a reference genome, effectively censoring them); it also assigns an error to an estimated binding location. The comparison study with existing programs on real ChIP-seq datasets (STAT1, NRSF, and ZNF143) demonstrates that the NEXT-peak model performs well both in calling peaks and locating them. The model also provides a goodness-of-fit test, to screen out spurious peaks and to infer multiple binding events in a region.ConclusionsThe NEXT-peak program calls peaks on any test dataset about as accurately as any other, but provides unusual accuracy in the estimated location of the peaks it calls. NEXT-peak is based on rigorous statistics, so its model also provides a principled foundation for a more elaborate statistical analysis of ChIP-seq data.
| S-EPMC3672025 | biostudies-literature
Project description:Exploring the metabolic and genetic control of gene expression on a genomic scale in yeast. This study is described in more detail in DeRisi JL et al. 1997. Science 278:680-6 Keywords: time-course
2002-02-12 | GSE28 | GEO
Project description:Yeast (Saccharomyces cerevisiae) has served as a key model system in biology and as a benchmark for "omics" technology. Although near-complete proteomes of log phase yeast have been measured, protein abundance in yeast is dynamic, particularly during the transition from log to stationary phase. Defining the dynamics of proteomic changes during this transition, termed the diauxic shift, is important to understand the basic biology of proliferative versus quiescent cells. Here, we perform temporal quantitative proteomics to fully capture protein induction and repression during the diauxic shift. Accurate and sensitive quantitation at a high temporal resolution and depth of proteome coverage was achieved using TMT10 reagents and LC-MS3 analysis on an Orbitrap Fusion tribrid mass spectrometer deploying synchronous precursor selection. Triplicate experiments were analyzed using the time-course R package and a simple template matching strategy was used to reveal groups of proteins with similar temporal patterns of protein induction and repression. Within these groups are functionally distinct types of proteins such as those of glyoxylate metabolism and many proteins of unknown function not previously associated with the diauxic shift (e.g. YNR034W-A and FMP16). We also perform a dual time-course experiment to determine Hap2-dependent proteins during the diauxic shift. These data serve as an important basic model for fermentative versus respiratory growth of yeast and other eukaryotes and are a benchmark for temporal quantitative proteomics.
| S-EPMC4563728 | biostudies-literature
Project description:The yeast Hsp31 mini-family proteins (Hsp31, Hsp32, Hsp33, Hsp34) belong to the highly conserved DJ-1 superfamily. The human DJ-1 protein is associated with cancer and neurodegenerative disorders, such as Parkinson’s disease. However, the precise function of human and yeast DJ-1 proteins is unclear. Here we show that the yeast DJ-1 homologs have a role in diauxic-shift, characterized by metabolic reprogramming due to glucose limitation. We find that the Hsp31 genes are strongly induced in diauxic-shift and in stationary phase (SP), and that deletion of these genes reduces chronological lifespan, impairs transcriptional reprogramming at diauxic-shift, and impairs the acquisition of several typical characteristics of SP, including autophagy induction. In addition, under carbon starvation, the HSP31 family gene deletion strains display impaired autophagy, disrupted TORC1 localization to P-bodies, and caused abnormal TORC1-mediated Atg13 phosphorylation. Repression of TORC1 by rapamycin in the gene deletion strains completely reversed their sensitivity to heat shock. Altogether, our data indicate that Hsp31 mini-family is required for diauxic-shift reprogramming and cell survival in SP, and plays a role upstream of TORC1. The enhanced understanding of the cellular function of these genes sheds light into the biological role of other members of the superfamily, including DJ-1, which is an attractive target for therapeutic intervention in cancer and in Parkinson’s disease. hsp31∆, hsp32∆, hsp33∆ are compared with its parental strain BY4741. We used One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling from Agilent.
2014-03-25 | GSE56124 | GEO
Project description:The yeast Hsp31 minifamily proteins (Hsp31, Hsp32, Hsp33, Hsp34) belong to the highly conserved DJ-1 superfamily. The human DJ-1 protein is associated with cancer and neurodegenerative disorders, such as Parkinson disease. However, the precise function of human and yeast DJ-1 proteins is unclear. Here we show that the yeast DJ-1 homologs have a role in diauxic-shift (DS), characterized by metabolic reprogramming because of glucose limitation. We find that the Hsp31 genes are strongly induced in DS and in stationary phase (SP), and that deletion of these genes reduces chronological lifespan, impairs transcriptional reprogramming at DS, and impairs the acquisition of several typical characteristics of SP, including autophagy induction. In addition, under carbon starvation, the HSP31 family gene-deletion strains display impaired autophagy, disrupted target of rapamycin complex 1 (TORC1) localization to P-bodies, and caused abnormal TORC1-mediated Atg13 phosphorylation. Repression of TORC1 by rapamycin in the gene-deletion strains completely reversed their sensitivity to heat shock. Taken together, our data indicate that Hsp31 minifamily is required for DS reprogramming and cell survival in SP, and plays a role upstream of TORC1. The enhanced understanding of the cellular function of these genes sheds light into the biological role of other members of the superfamily, including DJ-1, which is an attractive target for therapeutic intervention in cancer and in Parkinson disease.
| S-EPMC4024926 | biostudies-literature
Project description:To investigate the effect of Tup1, Xbp1, Isw2, and Sds3 on transcription we generated knockout strains and measured their transcript abundance compared to wild type during diauxic shift and stationary phase.
2022-08-17 | GSE210930 | GEO