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Time-resolved transcriptomics of S. cerevisiae and S. pastorianus in response to plasma membrane stresses

ABSTRACT: Time-resolved transcriptomics of S. cerevisiae and S. pastorianus in response to plasma membrane stresses

PROVIDER: PRJNA1249005 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR33090500_1.fastq.gz	Fastqsanger.gz
	SRR33090500_2.fastq.gz	Fastqsanger.gz
	SRR33090501_1.fastq.gz	Fastqsanger.gz
	SRR33090501_2.fastq.gz	Fastqsanger.gz
	SRR33090502_1.fastq.gz	Fastqsanger.gz

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Time-resolved transcriptomics of S. cerevisiae and S. pastorianus in response to plasma membrane stresses

Project description:Yeasts are beneficial microorganisms for human society and are utilized for academic and industrial purposes. For academic purposes, S. cerevisiae is a well-investigated model for studying eukaryotic cellular processes. For industrial purposes, S. pastorianus, which has a hybrid genome of S. cerevisiae and S. eubayanus, has been served for lager beer production. During fermentation, S. pastorianus produces ~7% of EtOH, which induces plasma membrane (PM)/cell wall stress in yeast. Therefore, S. pastorianus may experience PM stress and adapt to the self-forming environment during fermentation. However, how yeast adapts to PM stress remains unclear. Here, we investigated the temporal cellular responses of S. cerevisiae and S. pastorianus during adaptation to PM stresses by time-resolved mRNA-seq analysis. Our data showed different transcriptional phenotypes between S. cerevisiae and S. pastorianus during adaptation. The results may reflect the distinct nature of the two yeasts that have evolved in different nutritional environments. The dataset presented here would provide a promising resource for studying the characteristic nature of these differentially domesticated yeasts upon PM stresses.

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Time-resolved miRNA-mRNA integrated analysis reveals the miRNA-mRNA networks underlying plasma membrane damage-dependent senescence and DNA damage response-dependent senescence in WI-38 normal human fibroblasts

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Project description:Plasma membrane damage-dependent senescence is a novel senescence subtype. Here, we compare the time-resolved proteomic profiles of plasma membrane damage-dependent senescence, DNA damage-dependent senescence, and replicative senescence to find the major differences between the senescence subtypes.

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Plasma Membrane Integrity Signaling

Project description:To understand the transcriptional response of mammalian cells to plasma membrane stress we induced partial loss of plasmid membrane integrity by chemogenetic induction of pore forming proteins (Gasderimin and MLKL) or treatment with the detergent digitonin. We monitored transcription with mRNAseq in the immediate hours after plasma membrane damage and identified conserved transcriptional programs.

2021-10-04 | GSE166538 | GEO

Discovery of plasma membrane associated RNAs through APEX-seq

Project description:In addition to nucleic acids, a variety of biomolecules have been found on the plasma membrane. Whereas, researchers have realized that RNA has the ability to bind to membrane vesicles in vitro and connect to the plasma membrane of the cell. Hence, the combination of high-throughput sequencing and in suit labelling methods provides approaches for large-scale identification of subcellular RNAs. Here, we applied the recently published method APEX-seq, and identified 75 plasma membrane-associated RNAs, of which lncRNA PMAR72 is located around the membrane. In addition, we observed that PMAR72 was concentrated into foci in specific membrane areas. Our findings will provide some new evidence to elaborate the relationship between RNA and the plasma membrane of mammalian cells.

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Maltotriose consumption by hybrid Saccharomyces pastorianus is heterotic and results from regulatory cross-talk between parental sub-genomes

Project description:S. pastorianus strains are hybrids of S. cerevisiae and S. eubayanus that have been domesticated for several centuries in lager-beer brewing environments. As sequences and structures of S. pastorianus genomes are being resolved, molecular mechanisms and evolutionary origin of several industrially relevant phenotypes remain unknown. This study investigates how maltotriose metabolism, a key feature in brewing, may have arisen in early S. eubayanus x S. cerevisiae hybrids. To address this question, we generated a near-complete genome assembly of Himalayan S. eubayanus strains of the Holarctic subclade. This group of strains have been proposed to be the origin of the S. eubayanus subgenome of current S. pastorianus strains. The Himalayan S. eubayanus genomes harbored several copies of an SeAGT1 -oligoglucoside transporter gene with high sequence identity to genes encountered in S. pastorianus. Although Himalayan S. eubayanus strains are unable to grown on maltose and maltotriose, their maltose-hydrolase and SeMALT1 and SeAGT1 maltose-transporter genes complemented the corresponding null mutants of S. cerevisiae. Expression, in a Himalayan S. eubayanus strain, of a functional S. cerevisiae maltose-metabolism regulator gene (MALx3) enabled growth on oligoglucosides. The hypothesis that the maltotriose-positive phenotype in S. pastorianus is a result of heterosis was experimentally tested by constructing a S. cerevisiae x S. eubayanus laboratory hybrid with a complement of maltose-metabolism genes that resembles that of current S. pastorianus strains. The ability of this hybrid to consume maltotriose in brewer's wort demonstrated regulatory cross talk between sub-genomes and thereby validated this hypothesis. These results provide experimental evidence of the evolutionary origin of an essential phenotype of lager-brewing strains and valuable knowledge for industrial exploitation of laboratory-made S. pastorianus-like hybrids.

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Project description:validation of S. pastorianus microarray and expression profiling of S. pastorianus

2009-02-27 | E-MEXP-1693 | biostudies-arrayexpress

Saccharomyces pastorianus strains comparison

Project description:Saccharomyces pastorianus is the yeast used to make lager beer; it is known to be an interspecific hybrid formed by the fusion between S. cerevisiae and S. bayanus genomes. This data set queries 17 S. pastorianus strains, collected at various times over the last 125 years from various breweries located in different geographical locations, which were obtained from CBS and DBVPG culture collections. The data in this set represent array-CGH experiments performed with these strains, using "2-species" custom Agilent arrays (the "2-species" arrays contain probes spaced every ~2 kb across the whole genomes of both S. cerevisiae and S. bayanus; the probes are unique and specific for each genome). The data set also contains 3 self-self hybridizations (S. cerevisiae + S. bayanus DNA mixed together in equimolar amounts, then labeled green or red in separate reactions, then hybridized to the "2-species" arrays) used for normalization in CGH-Miner analysis. A strain or line experiment design type assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species.

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Enhanced flavour profiles through radicicol induced genomic variation in S. pastorianus lager yeast

Project description:We report the gene expression profile of two polypolid Saccharomyces pastorianus mutants obtained by random mutagenesis using radicicol. Mutants derived from the Group I strain CBS1538 and the Group II strain W34/70. Saccharomyces pastorianus is a hybrid of Saccharomuyces cerevisiaie and Saccharomyces eubayanus. We report changes in transcriptome of the mutants compared to their respective parental strain

2022-09-30 | GSE205364 | GEO

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