Dormancy-to-death transition in yeast spores occurs due to gradual loss of gene-expressing ability
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ABSTRACT:
PROVIDER: PRJNA669762 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12833300.fastq.gz | Fastqsanger.gz | |||
| SRR12833301.fastq.gz | Fastqsanger.gz | |||
| SRR12833302.fastq.gz | Fastqsanger.gz | |||
| SRR12833303.fastq.gz | Fastqsanger.gz | |||
| SRR12833304.fastq.gz | Fastqsanger.gz |
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Project description:Dormancy is colloquially considered as extending lifespan by being still. Starved yeasts form dormant spores that wake-up (germinate) when nutrients reappear but cannot germinate (die) after some time. What sets their lifespans and how they age are open questions because what processes occur - and by how much - within each dormant spore remains unclear. With single-cell-level measurements, we discovered how dormant yeast spores age and die: spores have a quantifiable gene-expressing ability during dormancy that decreases over days to months until it vanishes, causing death. Specifically, each spore has a different probability of germinating that decreases because its ability to - without nutrients - express genes decreases, as revealed by a synthetic circuit that forces GFP expression during dormancy. Decreasing amounts of molecules required for gene expression - including RNA polymerases - decreases gene-expressing ability which then decreases chances of germinating. Spores gradually lose these molecules because they are produced too slowly compared to their degradations, causing gene-expressing ability to eventually vanish and, thus, death. Our work provides a systems-level view of dormancy-to-death transition.
2020-10-20 | GSE159575 | GEO
Project description:Dormancy is colloquially considered as extending lifespan by being still. Starved yeasts form dormant spores that wake-up (germinate) when nutrients reappear but cannot germinate (die) after some time. What sets their lifespans and how they age are open questions because what processes occur-and by how much-within each dormant spore remains unclear. With single-cell-level measurements, we discovered how dormant yeast spores age and die: spores have a quantifiable gene-expressing ability during dormancy that decreases over days to months until it vanishes, causing death. Specifically, each spore has a different probability of germinating that decreases because its ability to-without nutrients-express genes decreases, as revealed by a synthetic circuit that forces GFP expression during dormancy. Decreasing amounts of molecules required for gene expression-including RNA polymerases-decreases gene-expressing ability which then decreases chances of germinating. Spores gradually lose these molecules because they are produced too slowly compared with their degradations, causing gene-expressing ability to eventually vanish and, thus, death. Our work provides a systems-level view of dormancy-to-death transition.
| S-EPMC7673291 | biostudies-literature
Project description:Mycobacterium tuberculosis employs several strategies to combat and adapt to adverse conditions encountered inside the host. The non-replicative dormant state of the bacterium is linked to drug resistance and slower response to anti-tubercular therapy. It is known that alterations in lipid content allow dormant bacteria to acclimatize to cellular stress. Employing comparative lipidomic analysis we profiled the changes in lipid metabolism in M. tuberculosis using a modified Wayne's model of hypoxia-induced dormancy. Further we subjected the dormant bacteria to resuscitation, and analyzed their lipidomes until the lipid profile was similar to that of normoxially grown bacteria. An enhanced degradation of cell wall-associated and cytoplasmic lipids during dormancy, and their gradual restoration during reactivation, were clearly evident. This study throws light on distinct lipid metabolic patterns that M. tuberculosis undergoes to maintain its cellular energetics during dormancy and reactivation.
2018-10-22 | MTBLS304 | MetaboLights
Project description:By entering a reversible state of reduced metabolic activity, dormant microorganisms are able to contend with suboptimal conditions that would otherwise reduce their fitness. In addition, certain types of dormancy like sporulation, can serve as a refuge from parasitic infections. Phages are unable to attach to spores, but their genomes can be entrapped in the resting structures and are able to resume infection upon host germination. Thus, dormancy has the potential to affect both the reproductive and survival components of phage fitness. Here, we characterized the distribution and diversity of sigma factors in nearly 3,500 phage genomes. Homologs of bacterial sigma factors that are responsible for directing transcription during sporulation were preferentially recovered in phages that infect spore-forming hosts. While non-essential for lytic infection, when expressed in Bacillus subtilis, we demonstrate that phage-encoded sigma factors activated sporulation gene networks and reduced spore yield. Our findings suggest that the acquisition of host-like transcriptional regulators may allow phages to manipulate the expression of complex traits, like the transitions involved in bacterial dormancy.
2021-11-05 | GSE187004 | GEO
Project description:Background: Bacterial spores can remain dormant for decades, yet harbor the exceptional capacity to rapidly resume metabolic activity and recommence life. Although germinants and their corresponding receptors have been known for more than 30 years, the molecular events underlying this remarkable cellular transition from dormancy to full metabolic activity are only partially defined. Results: Here, we examined whether protein phospho-modifications occur during germination, the first step of exiting dormancy, thereby facilitating spore revival. Utilizing Bacillus subtilis as a model organism, we performed phosphoproteomic analysis to define the Ser/Thr/Tyr phosphoproteome of a reviving spore. The phosphoproteome was found to chiefly comprise newly identified phosphorylation sites located within proteins involved in basic biological functions, such as transcription, translation, carbon metabolism and spore-specific determinants. Quantitative comparison of dormant and germinating spore phosphoproteomes revealed phosphorylation dynamics, indicating that phospho-modifications could modulate protein activity during this cellular transition. Furthermore, by mutating select phosphorylation sites located within proteins representative of key biological processes, we established a functional connection between phosphorylation and the progression of spore revival. Conclusions: In this study we provide for the first time a phosphoproteomic view of a germinating bacterial spore. We show that the spore phosphoproteome is dynamic and present evidence that phosphorylation events play an integral role in facilitating spore revival.
2015-08-27 | PXD002559 | Pride
Project description:Spores of Bacillales and Clostridiales species contain 100s of different mRNAs, and their major function in Bacillus subtilis is to provide ribonucleotides for new RNA synthesis when spores germinate. In new work, RNA was isolated from spores of five Bacillales and one Clostridioides species and relative spore mRNA levels were determined by RNA-seq. Determination of RNA levels in single spores allowed calculation of RNA nt/spore, and assuming mRNA is 3% of spore RNA allowed calculation that only ~6% of spore mRNAs were present at ≥ 1/spore. Bacillus subtilis, Bacillus atrophaeus and Clostridioides difficile spores had 49, 42 and 51 mRNAs at >1/spore, respectively. Numbers of mRNAs at ≥1/spore were ~10 to 50% higher in Geobacillus stearothermophilus and Bacillus thuringiensis Al Hakam spores, respectively, and ~ 4-fold higher in Bacillus megaterium spores. Notably, in all species: i) many of the 60 most abundant spore mRNAs were transcribed by RNA polymerase with forespore-specific s factors; ii) some to many of the most abundant spore mRNAs encoded orthologs of those encoded by abundant B. subtilis spore mRNAs and proteins present in dormant spores ; and iii) some spore mRNAs were likely transcribed in the mother cell compartment of the sporulating cell. Indeed , analysis of the coverage of RNA-seq reads on mRNAs from all six species suggested that abundant spore mRNAs were at least somewhat fragmented. This observation was confirmed by RT-qPCR analysis of three abundant mRNAs each from B. subtilis and C. difficile spores. These data add to a growing body of evidence indicating that the great majority of mRNAs in spores of Firmicutes are degradation and function as a ribonucleotide depot for new RNA synthesis when spores germinate.
2021-05-05 | GSE173854 | GEO
Project description:Tuberculosis, caused by Mycobacterium tuberculosis, still remains a major global health problem. The main obstacle in eradicating this disease is the ability of this pathogen to remain dormant in macrophages, and to get reactivated later under immuno-compromised conditions. The physiology of hypoxic nonreplicating M. tuberculosis is well studied using many in vitro dormancy models. However, the physiological changes that take place during the shift from dormancy to aerobic growth (reactivation) have rarely been subjected to a detailed investigation. In this study, we developed an in vitro reactivation system by re-aerating bacteria that were made dormant employing Wayne’s dormancy model, and compared the proteome profiles of dormant and reactivated bacteria using label-free one-dimensional LC/MS/MS analysis.
2015-06-01 | PXD001158 | Pride
Project description:Because of their ubiquity and resistance to spacecraft decontamination, bacterial spores are considered likely potential forward contaminants on robotic missions to Mars. Thus it is important to understand their global responses to long-term exposure to space or Mars environments. As part of the PROTECT experiment, spores of B. subtilis 168 were exposed to real space conditions and to simulated martian conditions for 559 days in low Earth orbit mounted on the EXPOSE-E exposure platform outside the European Columbus module on the International Space Station. Upon return, spores were germinated, total RNA extracted and fluorescently labeled, and used to probe a custom Bacillus subtilis microarray to identify genes preferentially activated or repressed relative to ground control spores. Increased transcript levels were detected for a number of stress-related regulons responding to DNA damage (SOS response, SPβ prophage induction), protein damage (CtsR/Clp system), oxidative stress (PerR regulon) and cell envelope stress (SigV regulon). Spores exposed to space demonstrated a much broader and more severe stress response than spores exposed to simulated Mars conditions. The results are discussed in the context of planetary protection for a hypothetical journey of potential forward contaminant spores from Earth to Mars and their subsequent residence on Mars.
2012-06-01 | GSE37124 | GEO
Project description:Delayed implantation occurs in many mammals, but the underlying mechanisms that direct this process remain largely unknown. In mice, ovariectomy prior to the preimplantation ovarian estrogen secretion on day 4 of pregnancy initiates blastocyst dormancy, which can be maintained for more than 200 days by continued progesterone Keywords: other
2004-08-04 | GSE1634 | GEO
Project description:This study investigated changes in the transcriptome of outdoor grown leafy spurge crown buds as they progress from paradormancy in August and September into endo dormancy in October through to ecodormancy in November and December. Keywords: Dormancy leafy spurge adventitious-buds
2007-08-24 | GSE8849 | GEO