Project description:Multi-omic absolute quantitative analysis of the yeast (Saccharomyces cerevisiae) mitotic cell cycle. Transcriptomics (RNA-Seq), proteomics (SILAC/ iBAQ), phosphoproteomics (SILAC/ iBAQ, enrichment with TiO2), and untargeted metabolomics (Metabolon, Inc.) were performed, all in biological triplicate. Three sub-projects from this central project were generated, in order of priority: (1) growth on glucose (n= 30 samples) (2) growth on ethanol (n= 21) and (3) pheromone effect (n= 51 samples; combined glucose and ethanol samples). For each sample, every omic type was analysed (n=4; transcriptomic, proteomic, phosphoproteomic, and metabolomic). Total omic samples generated for project = 204.
Project description:We use Saccharomyces cerevisiae, grown on glucose and synchronized with CDC15-2, to map interactions of different cellular processes during the yeast cell cycle.
Project description:We investigate the mechanism by which glucose restriction extends yeast replicative lifespan, using an approach that combines ribosomal profiling and RNA-seq. We systematically compared the translational and transcriptional profiles of cells grown in glucose restriction and normal media, uncovering groups of functionally related genes that are up or down regulated.
Project description:The sexual cycle of Ustilago maydis includes the succession of a saprophytic haploid yeast stage to a virulent hyphal dikaryotic stage, product of the mating of sexually compatible yeast cells. This dimorphic transition may be replicated in vitro by different means. Recently, it was shown that ethanol induced filamentous growth on solid medium, and we observed that this process also occurred in liquid media. Since the utilization of a six- or a two-carbon source involves different metabolic pathways, we considered that the morphogenetic process might be associated with this alteration. Accordingly, we analyzed the transcriptome of U. maydis grown in glucose or in ethanol using the Illumina RNA Seq. Around 18 million reads were obtained from each treatment. From the 6788 U. maydis genes, 542 were differentially expressed (158 upregulated and 384 downregulated) during incubation with ethanol compared to glucose-grown cells, revealing a noticeable alteration in the metabolism of the fungus through their adaptation to either carbon source. The present phenomenon is a further example of how an alteration in a two-dimensional mechanism (metabolism) can affect a three-dimensional process (cell morphogenesis).
Project description:Strand-specific RNA-seq libraries were constructed for two samples, including (I) wild-type strain NBRC0988 grown in YEP medium containing 2% w/v glucose;(II) wild-type strain NBRC0988 grown in YEP medium containing 2% w/v xylose. For preparation of RNA samples, NBRC0988 cells grown overnight were inoculated into 100 ml liquid Yeast Extract Peptone Dextrose (YEPD) medium with the initial inoculation amount of OD600= 0.1, and cultured for 15 hours at 30℃ and 250 rpm. The cells were collected by centrifugation at 6,000g for 5 minutes. After washing twice with phosphate buffer saline (PBS), they were inoculated into new 100 mL YEP medium containing 2% w/v glucose or xylose.After flask culturing at 30°C and 250 rpm for an additional 5 hours, the yeast cells were collected by centrifugation for total RNA isolation and Illumina RNA-seq library construction. Total RNA for samples were isolated using TRIzol reagent (Invitrogen, Grand Island, USA), then used for high-throughput RNA sequencing. The 150-nt paired-end strand-specific RNA-seq libraries (SS_lib_type RF) were generated commercially at Novogene Biotechnology Co. Ltd (Tianjin, China) by using Illumina’s novaseq 6000 platform (Illumina, San Diego, USA).
Project description:Carbon source is the basic nutrition and is essential for yeast growth. We grew the yeast cells (BY4741 strain) under different carbon sources including glucose with different concentration, galactose and raffinose. We generated bulk-cell RNA-seq data and investigated the dynamics of gene expression profiles under different growth conditions. We also generated single-cell RNA-seq data for yeast cells under 2% glucose, and explored the heterogeneity of gene expression within a cell population.