Slowest possible replicative life at frigid temperatures for yeast
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA872556 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21228200_1.fastq.gz | Fastqsanger.gz | |||
| SRR21228200_2.fastq.gz | Fastqsanger.gz | |||
| SRR21228201_1.fastq.gz | Fastqsanger.gz | |||
| SRR21228201_2.fastq.gz | Fastqsanger.gz | |||
| SRR21228202_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 218 |
Similar Datasets
Project description:Microbes and animals often inhabit frigid environments. Little is known about the design principles that govern a cell’s slow progression in life – how it proliferates, ages and dies – and potential constraints on slowly progressing life. Challenges lie in monitoring slow, intracellular processes and quantifying their combined effects on cells. Here we use budding yeast to quantitatively establish principles that govern cell proliferation and survival at near-freezing temperatures (0C – 5C). By monitoring individual cells for months at near-freezing temperatures, we found small numbers of cells dividing with weeks-long doubling times, while most others died. We found that cells die and cannot divide primarily from having high levels of Reactive Oxygen Species (ROS). Reducing ROS levels or enabling G1 exit with abundant ROS largely prevented deaths and enabled cell divisions with shortened doubling times. These perturbations yielded a comprehensive view of cell's life at near-freezing temperatures that integrated our measurements of single cells’ lifespans, days-to-months-long cell-cycle durations, protein-synthesis rates, and genome-wide transcription rates. With a mathematical model, this systems-level view revealed that protein-synthesis dynamics becomes more rate-limiting for cell duplication while mRNA-synthesis dynamics becomes less rate-limiting as temperature approaches 0C. Consequently, the protein-synthesis rate and ROS together establish low-speed and high-speed limits for life at near-freezing temperatures: shortest and longest possible doubling times. Progressing through cell cycle more slowly than the low-speed limit ensures death. This work establishes a quantitative, systems-level foundation for engineering organisms to live in frigid environments and elucidating fundamental limits to slowing down life.
2022-11-13 | GSE211918 | GEO
Project description:Determining whether life can progress arbitrarily slowly may reveal fundamental barriers to staying out of thermal equilibrium for living systems. By monitoring budding yeast's slowed-down life at frigid temperatures and with modeling, we establish that Reactive Oxygen Species (ROS) and a global gene-expression speed quantitatively determine yeast's pace of life and impose temperature-dependent speed limits - shortest and longest possible cell-doubling times. Increasing cells' ROS concentration increases their doubling time by elongating the cell-growth (G1-phase) duration that precedes the cell-replication (S-G2-M) phase. Gene-expression speed constrains cells' ROS-reducing rate and sets the shortest possible doubling-time. To replicate, cells require below-threshold concentrations of ROS. Thus, cells with sufficiently abundant ROS remain in G1, become unsustainably large and, consequently, burst. Therefore, at a given temperature, yeast's replicative life cannot progress arbitrarily slowly and cells with the lowest ROS-levels replicate most rapidly. Fundamental barriers may constrain the thermal slowing of other organisms' lives.
| S-EPMC9726825 | biostudies-literature
Project description:Yeast transcriptome profiling in replicative ageing
| PRJEB9510 | ENA
Project description:A crucial step towards understanding the mechanisms underlying aging is to obtain an integrated account of the molecular changes during aging. To address this, we mapped the yeast (S. cerevisiae) transcriptome during the replicative lifespan of budding yeast using novel culture and computational methods.
2015-10-06 | E-MTAB-3605 | biostudies-arrayexpress
Project description:Protein synthesis is strictly regulated during replicative aging in yeast, but global translational regulation during replicative aging is poorly characterized. To conduct ribosomal profiling during replicative aging, we collected a large number of dividing aged cells using a miniature chemostat aging device. Translational efficiency, defined as the number of ribosome footprints normalized to transcript abundance, was compared between young and aged cells for each gene. We identified more than 700 genes with changes greater than twofold during replicative aging. Increased translational efficiency was observed in genes involved in DNA repair and chromosome organization. Decreased translational efficiency was observed in genes encoding ribosome components, transposon Ty1 and Ty2 genes, transcription factor HAC1 genes associated with the unfolded protein response, genes involved in cell wall synthesis and assembly, and ammonium permease genes. Our results provide a global view of translational regulation during replicative aging, in which the pathways involved in various cell functions are translationally regulated and cause diverse phenotypic changes.
2022-09-25 | GSE203147 | GEO
Project description:Multifarious translational regulation during replicative aging in yeast
| PRJNA838843 | ENA
Project description:A quantitative genetic analysis of the yeast replicative life span was carried out by sampling the natural genetic variation
2012-07-18 | GSE37590 | GEO
Project description:In this study we perform ATAC-seq of budding yeast strains with variable copy number of the rRNA genes (rDNA CN). We aim to better understand the relationship between DNA accessibility and replicative lifespan in strains with variable rDNA CN.
2022-04-05 | GSE193598 | GEO
Project description:We use ribosome footprinting to assess the gene expression changes occuring after 10 minutes of heat stress at either 40°C or 42°C compared to non-stressed yeast cells (30°C). We find that between 40°C and 42°C there is a shift in gene expression from the expression of genes harboring long and structured 5'UTRs to the expression of genes harboring thranscripts with short and unstructure 5'UTRs. We performed these experiments for WT yeast cells as well as for mutant yeast cells in which the RNA helicase Ded1 condensates at lower temperatures (Ded1-IDRm). We find upon comparing mutant and WT cells at 42°C, that Ded1-IDRm has increased expression of genes harboring unstructured 5'UTRs and decreased expression of genes harboring structured 5'UTRs.
2020-04-30 | GSE131176 | GEO
Project description:All eukaryotic cells divide a finite number of times, termed replicative aging, but the reason for this is not clear. Consistent with the decreased total histone protein levels in aged Saccharomyces cerevisiae, which is a cause of aging (1), we find that nucleosome occupancy decreases 50% across the whole genome during replicative aging by spike-in controlled MNase sequencing. Nucleosomes become fuzzier or move to sequences predicted to better accommodate histone octamers. All yeast genes are induced during aging. Genes that are repressed in young cells are most induced, accompanied by nucleosome loss from their promoters that have unique chromatin organization. Contrary to the loss of mitochondrial function during aging, mitochondrial DNA content increases and unprecedented levels of large-scale chromosomal alterations and increased retrotransposition are observed. Mnase-Seq experiments were carried out for young yeast, old yeast, and old yeast with histone over expression, 3 replicates were done for each category. RNA-Seq were carried out for the same categories of yeast cells but with 2 replicates for each. Genome-Seq were done for the young and old yeast with 2 replicates for each.
2014-02-26 | E-GEOD-47023 | biostudies-arrayexpress